@datagrok/helm 2.13.8 → 3.0.1

package/dist/94.js.map

@@ -0,0 +1 @@
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s==\"number\"&&Number.isInteger(s)||t.push({path:`${e}.id`,message:`Expected integer or string, got ${F(s)}`});}if(\"meta\"in i&&i.meta!==void 0){let s=i.meta;Qe(s)?s.colors!==void 0&&rr(s.colors,`${e}.meta.colors`,t):t.push({path:`${e}.meta`,message:`Expected object, got ${F(s)}`});}}function ir(i,e,t,n){if(!Qe(i)){t.push({path:e,message:`Expected an object, got ${F(i)}`});return}let o=i.label;if(o===void 0?t.push({path:`${e}.label`,message:\"Required property missing\"}):typeof o!=\"string\"?t.push({path:`${e}.label`,message:`Expected string, got ${F(o)}`}):nr.test(o)?n.has(o)?t.push({path:`${e}.label`,message:`Duplicate R-group label '${o}'`}):n.add(o):t.push({path:`${e}.label`,message:`Expected pattern /^R[1-9][0-9]*$/, got '${o}'`}),ln(i,\"capGroupName\",e,t),Je(i)===void 0){let r=Object.keys(i).some(s=>s.toLowerCase()===\"capgroupsmiles\");t.push({path:`${e}.capGroupSMILES`,message:r?\"Expected string\":\"Required property missing\"});}Ze(i,\"alternateId\",e,t),\"id\"in i&&i.id!==void 0&&(typeof i.id!=\"number\"||!Number.isInteger(i.id))&&t.push({path:`${e}.id`,message:`Expected integer, got ${F(i.id)}`});}function rr(i,e,t){if(!Qe(i)){t.push({path:e,message:`Expected object, got ${F(i)}`});return}for(let n of [\"default\",\"light\",\"dark\"])i[n]!==void 0&&sr(i[n],`${e}.${n}`,t);}function sr(i,e,t){if(!Qe(i)){t.push({path:e,message:`Expected object, got ${F(i)}`});return}for(let n of [\"line\",\"text\",\"background\"])i[n]===void 0?t.push({path:`${e}.${n}`,message:\"Required property missing\"}):typeof i[n]!=\"string\"&&t.push({path:`${e}.${n}`,message:`Expected string, got ${F(i[n])}`});}function ln(i,e,t,n,o){let r=i[e],s=`${t}.${e}`;if(r===void 0){n.push({path:s,message:\"Required property missing\"});return}if(typeof r!=\"string\"){n.push({path:s,message:`Expected string, got ${F(r)}`});return}o?.minLength!==void 0&&r.length<o.minLength&&n.push({path:s,message:`Expected string of length >= ${o.minLength}, got ${r.length}`});}function Ze(i,e,t,n){let o=i[e];o!==void 0&&typeof o!=\"string\"&&n.push({path:`${t}.${e}`,message:`Expected string, got ${F(o)}`});}function Qe(i){return typeof i==\"object\"&&i!==null&&!Array.isArray(i)}function F(i){return i===null?\"null\":Array.isArray(i)?\"array\":typeof i}var ar=/^R([1-9][0-9]*)$/;function ee(i){switch(i.polymerType){case v.PEPTIDE:return b.AA;case v.CHEM:return b.CHEM;case v.BLOB:return b.BLOB;case v.RNA:{if(i.monomerType===\"Branch\")return b.BASE;if(i.monomerType===\"Backbone\"){let e=i.naturalAnalog;return e===\"P\"||e===\"p\"?b.LINKER:b.SUGAR}return null}default:return null}}function lr(i){let e=new Map;for(let t of i.rgroups){let n=ar.exec(t.label);n!==null&&e.set(parseInt(n[1],10),t);}return Object.assign({},i,{rs:i.rgroups.length,rgroupMap:e})}var dn=class i{constructor(e){this._version=0;this._byPolymerSymbol=new Map;this._byBiotypeSymbol=new Map;this._byNaturalAnalog=new Map;this._resolved=new WeakMap;this._inlineSmilesCounter=0;this.source=e,this.onChanged=new Z;}static empty(e=\"empty\"){return new i(e)}static fromJSON(e,t=\"inline\",n){let o=new i(t);for(let r=0;r<e.length;r++){let s=e[r],a=kt([s]);if(!a.ok){n!==void 0?n.skipped.push({index:r,errors:a.errors}):console.warn(`MonomerLib.fromJSON: skipping invalid entry at index ${r}`,a.errors);continue}o._addNoFire(s);}return o}static fromText(e,t=\"inline\"){let n;try{n=JSON.parse(e);}catch(r){let s=r instanceof Error?r.message:String(r);throw new I(\"invalid-monomer-lib\",`MonomerLib.fromText: JSON.parse failed \\u2014 ${s}`)}let o=kt(n);if(!o.ok)throw new I(\"invalid-monomer-lib\",`MonomerLib.fromText: schema validation failed (${o.errors.length} errors)`,{errors:o.errors});return i.fromJSON(o.data,t)}static async fromUrl(e,t){let n=t??globalThis.fetch;if(n===void 0)throw new I(\"fetch-unavailable\",\"MonomerLib.fromUrl: no fetch implementation available \\u2014 pass `fetchImpl` or run in a fetch-capable environment.\",{url:e});let o=await n(e);if(!o.ok)throw new I(\"monomer-lib-fetch-failed\",`MonomerLib.fromUrl: HTTP ${o.status} fetching ${e}`,{url:e,status:o.status});let r=await o.text();return i.fromText(r,e)}static merge(...e){let t=e.map(o=>o.source).join(\"+\")||\"empty\",n=new i(t);for(let o of e)for(let r of o.getPolymerTypes())for(let s of o.getMonomerSymbolsByType(r)){let a=o.getMonomer(r,s);a!==null&&n._addNoFire(a);}return n}get isEmpty(){for(let e of this._byPolymerSymbol.values())if(e.size>0)return  false;return  true}get version(){return this._version}getMonomer(e,t){let n=this._byPolymerSymbol.get(e);return n===void 0?null:n.get(t)??null}getMonomerSet(e){let t=this._byBiotypeSymbol.get(e);return t===void 0?new Map:new Map(t)}getMonomerSymbolsByType(e){let t=this._byPolymerSymbol.get(e);return t===void 0?[]:Array.from(t.keys())}getByNaturalAnalog(e,t){let n=this._byNaturalAnalog.get(e);if(n===void 0)return [];let o=n.get(t);return o===void 0?[]:o.slice()}getPolymerTypes(){let e=[];for(let[t,n]of this._byPolymerSymbol.entries())n.size>0&&e.push(t);return e}getColors(e,t){let n=dr(t),o=e===null?b.AA:ee(e)??b.AA;return $(e,o,n)}getResolved(e){return this._resolved.get(e)}addMonomer(e){let t=kt([e]);if(!t.ok)throw new I(\"invalid-monomer\",\"MonomerLib.addMonomer: schema validation failed\",{errors:t.errors});let n=this._addNoFire(e);this._bumpVersion(),this.onChanged.next({type:n?\"update\":\"add\",affectedSymbols:[e.symbol]});}addMonomers(e){let t=[],n=false;for(let o of e)this._addNoFire(o)&&(n=true),t.push(o.symbol);t.length!==0&&(this._bumpVersion(),this.onChanged.next({type:n?\"update\":\"add\",affectedSymbols:t}));}removeMonomer(e,t){let n=this._byPolymerSymbol.get(e);if(n===void 0)return  false;let o=n.get(t);if(o===void 0)return  false;n.delete(t);let r=ee(o);if(r!==null){let a=this._byBiotypeSymbol.get(r);a!==void 0&&a.delete(t);}let s=o.naturalAnalog;if(s!==void 0&&s!==\"\"){let l=this._byNaturalAnalog.get(e)?.get(s);if(l!==void 0){let d=l.indexOf(o);d>=0&&l.splice(d,1);}}return this._bumpVersion(),this.onChanged.next({type:\"remove\",affectedSymbols:[t]}),true}setMonomerColors(e,t,n){let o=this.getMonomer(e,t);if(o===null)throw new I(\"monomer-not-found\",`MonomerLib.setMonomerColors: ${e}/${t} not found`,{polymerType:e,symbol:t});let r=o.meta??{},s=r.colors??{},a=Object.assign({},r,{colors:Object.assign({},s,n)}),l=Object.assign({},o,{meta:a});this._addNoFire(l),this._bumpVersion(),this.onChanged.next({type:\"update\",affectedSymbols:[t]});}merge(e){for(let t of e.getPolymerTypes())for(let n of e.getMonomerSymbolsByType(t)){let o=e.getMonomer(t,n);o!==null&&this._addNoFire(o);}this._bumpVersion(),this.onChanged.next({type:\"reload\"});}registerInlineSmilesMonomer(e,t,n){let o=Yn(t);if(!o.ok)throw new I(\"inline-smiles-without-r-groups\",`MonomerLib.registerInlineSmilesMonomer: ${o.reason}`,{smiles:t});this._inlineSmilesCounter+=1;let r=`#${this._inlineSmilesCounter}`,s=[],a=Array.from(o.info.rgroupPositions.keys()).sort((c,u)=>c-u);for(let c of a)s.push({label:`R${c}`,capGroupName:\"H\",capGroupSMILES:\"\"});let l=n?.symbolHint!==void 0?{smilesHint:n.symbolHint}:void 0,d={symbol:r,polymerType:e,monomerType:\"Undefined\",molfile:\"\",smiles:o.canonicalSmiles,rgroups:s,...l!==void 0?{meta:l}:{}};return this._addNoFire(d),this._bumpVersion(),this.onChanged.next({type:\"add\",affectedSymbols:[r]}),d}toJSON(){let e=[];for(let t of this._byPolymerSymbol.values())for(let n of t.values())e.push(n);return e}_addNoFire(e){e=ao(e);let t=e.polymerType,n=this._byPolymerSymbol.get(t);n===void 0&&(n=new Map,this._byPolymerSymbol.set(t,n));let o=n.get(e.symbol);if(n.set(e.symbol,e),o!==void 0){let a=ee(o);if(a!==null){let d=this._byBiotypeSymbol.get(a);d!==void 0&&d.delete(o.symbol);}let l=o.naturalAnalog;if(l!==void 0&&l!==\"\"){let d=this._byNaturalAnalog.get(t)?.get(l);if(d!==void 0){let c=d.indexOf(o);c>=0&&d.splice(c,1);}}this._resolved.delete(o);}let r=ee(e);if(r!==null){let a=this._byBiotypeSymbol.get(r);a===void 0&&(a=new Map,this._byBiotypeSymbol.set(r,a)),a.set(e.symbol,e);}let s=e.naturalAnalog;if(s!==void 0&&s!==\"\"){let a=this._byNaturalAnalog.get(t);a===void 0&&(a=new Map,this._byNaturalAnalog.set(t,a));let l=a.get(s);l===void 0&&(l=[],a.set(s,l)),l.push(e);}return this._resolved.set(e,lr(e)),o!==void 0}_bumpVersion(){this._version+=1;}};function dr(i){return i===\"dark\"?Be:we}function xe(i,e,t){return new cn(i,e,t??{}).run()}var cr=new Set([\"?\",\"*\",\"_\",\"X\",\"N\"]),ur=/^R([1-9][0-9]*)$/;function mr(i){return typeof i.registerInlineSmilesMonomer==\"function\"}var cn=class{constructor(e,t,n){this.diagnostics=[];this.oldToNew=new Map;this.placeholderCache=new Map;this.mol=e,this.lib=t,this.options=n;}run(){let e=new Map;for(let a of this.mol.chains)e.set(a.id,a.polymerType);for(let a of this.mol.atoms){let l=e.get(a.bio.chainId)??null,d=this.resolveAtom(a,l);this.oldToNew.set(a.id,d);}for(let a of this.mol.atoms){let l=this.oldToNew.get(a.id);if(l===void 0||a.branchAtom===void 0)continue;let d=this.oldToNew.get(a.branchAtom.id);d!==void 0&&(l.branchAtom=d);}let t=[];for(let a of this.mol.bonds){let l=this.oldToNew.get(a.a1.id),d=this.oldToNew.get(a.a2.id);l===void 0||d===void 0||t.push({...a,a1:l,a2:d});}let n=new Map;for(let a of t)n.set(a.id,a);let o=[];for(let a of this.mol.chains){let l=[];for(let c of a.backboneAtoms){let u=this.oldToNew.get(c.id);u!==void 0&&l.push(u);}let d=[];for(let c of a.bonds){let u=n.get(c.id);u!==void 0&&d.push(u);}o.push({id:a.id,polymerType:a.polymerType,backboneAtoms:l,bonds:d,...a.annotation!==void 0?{annotation:a.annotation}:{},...a.strandType!==void 0?{strandType:a.strandType}:{}});}return {mol:{atoms:this.mol.atoms.map(a=>this.oldToNew.get(a.id)),bonds:t,chains:o,groups:this.mol.groups,annotations:this.mol.annotations},diagnostics:this.diagnostics}}resolveAtom(e,t){let n=null,o=e.biotype;if(t!==null){let r=this.lib.getMonomer(t,e.symbol);if(r!==null)n=this.toResolved(r),o=ee(r)??e.biotype;else if(this.isAmbiguitySymbol(e))n=this.synthesizeAmbiguity(t,e),this.emit(\"info\",\"ambiguous-monomer\",`Ambiguous monomer '${e.symbol}' on chain '${e.bio.chainId}'`,e);else if(Ce(e.symbol))n=this.registerInlineSmilesFallback(t,e);else if(this.options.legacyCaseFallback===true&&t===\"RNA\"){let s=this.findCaseInsensitiveMatch(t,e.symbol);s!==null&&(n=this.toResolved(s),o=ee(s)??e.biotype,this.emit(\"info\",\"case-mismatch\",`Symbol '${e.symbol}' matched library entry '${s.symbol}' only after case fold`,e));}n===null&&(n=this.synthesizeMissing(t,e),this.emit(\"warning\",\"unresolved-monomer\",`Monomer '${e.symbol}' not found in library for ${t}`,e));}return {...e,monomer:n,biotype:o}}toResolved(e){let t=this.lib.getResolved?.(e);if(t!==void 0)return t;let n=new Map;for(let o of e.rgroups){let r=ur.exec(o.label);r!==null&&n.set(parseInt(r[1],10),o);}return Object.assign({},e,{rs:e.rgroups.length,rgroupMap:n})}isAmbiguitySymbol(e){return !!(cr.has(e.symbol)||e.bio.ambiguity!==void 0)}synthesizeAmbiguity(e,t){let n=`ambig:${e}:${t.symbol}`,o=this.placeholderCache.get(n);return o===void 0&&(o={symbol:t.symbol,polymerType:e,monomerType:\"Undefined\",molfile:\"\",rgroups:[{label:\"R1\",capGroupName:\"H\",capGroupSMILES:\"\"},{label:\"R2\",capGroupName:\"H\",capGroupSMILES:\"\"}],meta:{ambiguous:true}},this.placeholderCache.set(n,o)),this.toResolved(o)}synthesizeMissing(e,t){let n=`missing:${e}:${t.symbol}`,o=this.placeholderCache.get(n);return o===void 0&&(o={symbol:t.symbol,polymerType:e,monomerType:\"Undefined\",molfile:\"\",rgroups:[{label:\"R1\",capGroupName:\"H\",capGroupSMILES:\"\"},{label:\"R2\",capGroupName:\"H\",capGroupSMILES:\"\"}],meta:{missing:true}},this.placeholderCache.set(n,o)),this.toResolved(o)}registerInlineSmilesFallback(e,t){if(mr(this.lib))try{let n=this.lib.registerInlineSmilesMonomer(e,t.symbol);return this.toResolved(n)}catch{this.emit(\"warning\",\"inline-smiles-without-r-groups\",`Inline SMILES '${pr(t.symbol,40)}' has no detectable R-groups`,t);}else this.emit(\"warning\",\"inline-smiles-without-r-groups\",\"Inline SMILES seen but lib has no registerInlineSmilesMonomer\",t);return this.synthesizeMissing(e,t)}findCaseInsensitiveMatch(e,t){let n=t.toLowerCase();for(let o of this.lib.getMonomerSymbolsByType(e))if(o.toLowerCase()===n&&o!==t){let r=this.lib.getMonomer(e,o);if(r!==null)return r}return null}emit(e,t,n,o){let r={chainId:o.bio.chainId,atomId:o.id,symbol:o.symbol};this.diagnostics.push({severity:e,code:t,message:n,context:r});}};function pr(i,e){return i.length<=e?i:i.slice(0,e-1)+\"\\u2026\"}function et(i,e,t){let n=t?.mode??\"lenient\",o;try{o=qn(i);}catch(r){if(r instanceof N){if(n===\"strict\")throw r;let s={severity:\"error\",code:r.code,message:r.message,...r.span!==void 0?{span:{start:r.span.start,end:r.span.end}}:{}};return {mol:me(),diagnostics:[s]}}throw r}return co(o,e,t)}function co(i,e,t){let o=new mn(i,e,t?.mode??\"lenient\").parseDocument();if(e===null||t?.resolveMonomers===false)return o;let r=xe(o.mol,e,{mode:t?.mode??\"lenient\",...t?.legacyCaseFallback===true?{legacyCaseFallback:true}:{}});return {mol:r.mol,diagnostics:[...o.diagnostics,...r.diagnostics]}}var un=class{constructor(e){this.tokens=e.tokens,this.len=e.tokens.length,this.eof=e.tokens[e.tokens.length-1],this.idx=0;}peek(e=0){let t=this.idx+e;return t>=this.len?this.eof:this.tokens[t]}advance(){let e=this.idx<this.len?this.tokens[this.idx]:this.eof;return e.kind!==\"eof\"&&(this.idx+=1),e}optional(e){let t=this.idx<this.len?this.tokens[this.idx]:this.eof;return t.kind===e?(t.kind!==\"eof\"&&(this.idx+=1),t):null}at(e){return (this.idx<this.len?this.tokens[this.idx]:this.eof).kind===e}at2(e,t){let o=(this.idx<this.len?this.tokens[this.idx]:this.eof).kind;return o===e||o===t}at3(e,t,n){let r=(this.idx<this.len?this.tokens[this.idx]:this.eof).kind;return r===e||r===t||r===n}currentSpan(){return (this.idx<this.len?this.tokens[this.idx]:this.eof).span}position(){return this.idx}setPosition(e){this.idx=e;}isAtEnd(){return (this.idx<this.len?this.tokens[this.idx]:this.eof).kind===\"eof\"}},hr=/^(PEPTIDE|RNA|DNA|CHEM|BLOB|G)([0-9]+)$/;function lo(i){let e=hr.exec(i);if(e===null)return null;let t=e[1],n=parseInt(e[2],10);switch(t){case \"PEPTIDE\":return {rawTypeName:\"PEPTIDE\",polymerType:v.PEPTIDE,number:n,isDnaShim:false,isGroup:false};case \"RNA\":return {rawTypeName:\"RNA\",polymerType:v.RNA,number:n,isDnaShim:false,isGroup:false};case \"DNA\":return {rawTypeName:\"DNA\",polymerType:v.RNA,number:n,isDnaShim:true,isGroup:false};case \"CHEM\":return {rawTypeName:\"CHEM\",polymerType:v.CHEM,number:n,isDnaShim:false,isGroup:false};case \"BLOB\":return {rawTypeName:\"BLOB\",polymerType:v.BLOB,number:n,isDnaShim:false,isGroup:false};case \"G\":return {rawTypeName:\"G\",polymerType:v.PEPTIDE,number:n,isDnaShim:false,isGroup:true};default:return null}}var mn=class{constructor(e,t,n){this.diagnostics=[];this.chains=[];this.chainById=new Map;this.pendingBonds=[];this.groups=[];this.atomIds=new _e;this.bondIds=new _e;this.cursor=new un(e),this.source=e.source,this.lib=t,this.mode=n,this.annotations={perPolymer:new Map,version:\"\"};}parseDocument(){if(this.cursor.isAtEnd())return this.emit(\"warning\",\"empty-helm\",\"Empty HELM string\"),{mol:me(),diagnostics:this.diagnostics};if(this.parseSimplePolymers(),this.expectDollarSeparator(1),this.parseConnections(),this.expectDollarSeparator(2),this.parseGroupsSection(),this.expectDollarSeparator(3),this.parseAnnotationsSection(),this.cursor.at(\"dollar\")&&(this.cursor.advance(),this.parseVersionTrailer()),!this.cursor.isAtEnd())for(this.emit(\"warning\",\"extra-section-separator\",\"Unexpected trailing tokens after HELM document\",this.cursor.currentSpan());!this.cursor.isAtEnd();)this.cursor.advance();return {mol:this.finalize(),diagnostics:this.diagnostics}}expectDollarSeparator(e){if(this.cursor.at(\"dollar\")){this.cursor.advance();return}this.emit(\"error\",\"missing-section-separator\",`Expected '$' separator before section ${e+1}`,this.cursor.currentSpan());}parseSimplePolymers(){if(!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()))for(this.parsePolymer();this.cursor.at(\"pipe\");){if(this.cursor.advance(),this.cursor.at(\"dollar\")||this.cursor.isAtEnd()){this.emit(\"warning\",\"empty-polymer-body\",\"Empty polymer after '|'\",this.cursor.currentSpan());return}this.parsePolymer();}}parsePolymer(){let e=this.cursor.currentSpan(),t=this.cursor.optional(\"identifier\");if(t===null){this.emit(\"error\",\"unexpected-token\",`Expected polymer id, got '${this.cursor.peek().value}'`,this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let n=lo(t.value);if(n===null){this.emit(\"error\",\"unknown-polymer-type\",`Unknown polymer type '${t.value}'`,t.span),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}if(this.chainById.has(t.value)&&this.emit(\"warning\",\"duplicate-polymer-id\",`Duplicate polymer id '${t.value}'`,t.span),this.cursor.optional(\"lbrace\")===null){this.emit(\"error\",\"unexpected-token\",`Expected '{' after polymer id '${t.value}'`,this.cursor.currentSpan());return}let o={id:t.value,polymerType:n.polymerType,rawTypeName:n.rawTypeName,rawNumber:n.number,backboneAtoms:[],allAtoms:[],bonds:[],span:{start:e.start,end:e.end}};if(this.chains.push(o),this.chainById.set(o.id,o),this.cursor.at(\"rbrace\"))this.emit(\"warning\",\"empty-polymer-body\",`Empty body for polymer '${o.id}'`,this.cursor.currentSpan());else if(n.isGroup)this.parseGroupBody(o);else switch(n.polymerType){case v.PEPTIDE:this.parsePeptideBody(o);break;case v.RNA:this.parseRnaBody(o,n.isDnaShim),n.isDnaShim&&this.emit(\"info\",\"dna-emitted-as-rna\",`DNA polymer '${o.id}' will be emitted as RNA on canonicalize`,t.span);break;case v.CHEM:this.parseChemBody(o);break;case v.BLOB:this.parseBlobBody(o);break;}if(this.cursor.optional(\"rbrace\")===null){this.emit(\"error\",\"unterminated-brace\",`Expected '}' to close polymer '${o.id}'`,this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let r=this.cursor.optional(\"quote-string\");r!==null&&(o.annotation=r.value);}parsePeptideBody(e){for(this.parsePeptideItem(e);this.cursor.at(\"dot\")&&(this.cursor.advance(),!(this.cursor.at(\"rbrace\")||this.cursor.at(\"gt\")));)this.parsePeptideItem(e);if(this.cursor.at(\"gt\")){let t=this.cursor.currentSpan();this.cursor.advance(),this.emit(\"warning\",\"peptide-cyclic-without-closure\",`Peptide '${e.id}' marked cyclic with '>' \\u2014 no explicit closure connection emitted`,t);}}parsePeptideItem(e){if(this.cursor.at(\"lparen\"))this.parsePeptideAlternation(e);else {let t=this.parsePeptideAtom(e);this.maybeRepeatBracket(e,[t]);}this.maybeAttachAnnotation(e);}parsePeptideAtom(e){let t=this.consumeMonomerSymbol(false),{symbol:n,annotation:o,ambiguity:r,ambiguityKind:s,isInlineSmiles:a,rawPayload:l,inlineSource:d,span:c}=t,u=this.makeAtom(e,b.AA,n);o!==void 0&&(u.tag=o),r!==void 0&&(u.bio.ambiguity=r),s!==void 0&&(u.bio.ambiguityKind=s),d!==void 0&&(u.inlineSource=d),a&&this.registerInlineSmiles(l,c,v.PEPTIDE),this.addToChain(e,u,true);let m=e.backboneAtoms[e.backboneAtoms.length-2];return m!==void 0&&this.addBond(e,m,u,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1}),u}parsePeptideAlternation(e){let t=this.cursor.currentSpan();if(this.cursor.advance(),this.peptideContentIsSubsequence()){let d=e.backboneAtoms.length;for(this.parsePeptideItem(e);this.cursor.at(\"dot\")&&(this.cursor.advance(),!(this.cursor.at(\"rparen\")||this.cursor.isAtEnd()));)this.parsePeptideItem(e);this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' to close repeat sub-sequence\",this.cursor.currentSpan());let c=e.backboneAtoms.slice(d);this.maybeRepeatBracket(e,c),this.maybeAttachAnnotation(e);return}let n=[],o=null;for(;!this.cursor.at(\"rparen\")&&!this.cursor.isAtEnd();){let d=this.parseAlternationCandidate(v.PEPTIDE);if(n.push(d),this.cursor.at(\"comma\"))o===\"and\"&&this.emit(\"warning\",\"mixed-separator-in-alternation\",\"Mixed ',' and '+' separators in alternation\",this.cursor.currentSpan()),o=\"or\",this.cursor.advance();else if(this.cursor.at(\"plus\"))o===\"or\"&&this.emit(\"warning\",\"mixed-separator-in-alternation\",\"Mixed ',' and '+' separators in alternation\",this.cursor.currentSpan()),o=\"and\",this.cursor.advance();else break}this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' to close alternation\",this.cursor.currentSpan());let r=o===\"and\"?\"+\":\",\",s=`(${n.map(d=>d.symbol+(d.ratio!==void 0?`:${String(d.ratio)}`:\"\")).join(r)})`,a=this.makeAtom(e,b.AA,\"?\");a.bio.ambiguity=s,a.bio.ambiguityKind=o===\"and\"?\"and\":\"or\",this.addToChain(e,a,true);let l=e.backboneAtoms[e.backboneAtoms.length-2];if(l!==void 0&&this.addBond(e,l,a,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1}),o===\"and\")for(let d of n)typeof d.ratio==\"number\"&&d.ratio<0&&this.emit(\"error\",\"ratio-and-negative\",`Negative ratio ${d.ratio} in AND mixture`,t);this.maybeRepeatBracket(e,[a]),this.maybeAttachAnnotation(e);}peptideContentIsSubsequence(){let e=1,t=0;for(;;){let n=this.cursor.peek(t);if(n.kind===\"eof\")return  false;if(n.kind===\"lparen\"){e+=1,t+=1;continue}if(n.kind===\"rparen\"){if(e-=1,e===0)return  true;t+=1;continue}if(e===1){if(n.kind===\"dot\")return  true;if(n.kind===\"comma\"||n.kind===\"plus\"||n.kind===\"colon\")return  false}if(t+=1,t>1024)return  false}}parseAlternationCandidate(e){let{symbol:t,isInlineSmiles:n,rawPayload:o,span:r}=this.consumeMonomerSymbol(true);n&&this.registerInlineSmiles(o,r,e);let s;if(this.cursor.optional(\"colon\")!==null){let a=this.cursor.peek();a.kind===\"integer\"||a.kind===\"decimal\"?(this.cursor.advance(),s=parseFloat(a.value)):a.kind===\"question\"?(this.cursor.advance(),s=\"?\"):this.emit(\"error\",\"unexpected-token\",\"Expected ratio after ':' in alternation\",a.span);}return s===void 0?{symbol:t}:{symbol:t,ratio:s}}parseRnaBody(e,t){for(this.parseRnaItem(e,t);this.cursor.at(\"dot\")&&(this.cursor.advance(),!(this.cursor.at(\"rbrace\")||this.cursor.at(\"dollar\")||this.cursor.isAtEnd()));)this.parseRnaItem(e,t);}parseRnaItem(e,t){if(this.cursor.at(\"lparen\")){this.parseRnaAlternation(e,t);return}if(this.cursor.at(\"asterisk\")){this.cursor.currentSpan();this.cursor.advance();let d=this.makeAtom(e,b.NUCLEOTIDE,\"*\");this.addToChain(e,d,true);let c=e.backboneAtoms[e.backboneAtoms.length-2];c!==void 0&&this.addBond(e,c,d,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1}),this.maybeRepeatBracket(e,[d]),this.maybeAttachAnnotation(e);return}let n=this.parseRnaSugar(e,t);this.maybeAttachAnnotation(e);let o;this.cursor.at(\"lparen\")&&(this.cursor.advance(),this.cursor.at(\"rparen\")||(o=this.parseRnaBaseSymbol(e),this.maybeAttachAnnotationTo(o)),this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' after RNA base\",this.cursor.currentSpan()),o!==void 0&&(this.addBond(e,n,o,\"branch\",{kind:\"numeric\",r:3},{kind:\"numeric\",r:1}),n.branchAtom=o));let r;this.canStartRnaLinker()&&(r=this.parseRnaLinker(e),this.maybeAttachAnnotationTo(r)),r!==void 0&&this.addBond(e,n,r,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1});let s=e.backboneAtoms.indexOf(n);if(s>0){let l=e.backboneAtoms[s-1];this.addBond(e,l,n,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1});}let a=[n];o!==void 0&&a.push(o),r!==void 0&&a.push(r),this.maybeRepeatBracket(e,a);}canStartRnaLinker(){let e=this.cursor.peek().kind;return e===\"identifier\"||e===\"inline-smiles\"||e===\"asterisk\"}parseRnaSugar(e,t){let{symbol:n,isInlineSmiles:o,rawPayload:r,inlineSource:s,span:a}=this.consumeMonomerSymbol(false),l=this.makeAtom(e,b.SUGAR,n);return s!==void 0&&(l.inlineSource=s),o&&this.registerInlineSmiles(r,a,v.RNA),this.addToChain(e,l,true),l}parseRnaBaseSymbol(e){let{symbol:t,isInlineSmiles:n,rawPayload:o,inlineSource:r,span:s}=this.consumeMonomerSymbol(false),a=this.makeAtom(e,b.BASE,t);return r!==void 0&&(a.inlineSource=r),n&&this.registerInlineSmiles(o,s,v.RNA),this.addToChain(e,a,false),a}parseRnaLinker(e){if(this.cursor.at(\"asterisk\")){this.cursor.currentSpan();this.cursor.advance();let d=this.makeAtom(e,b.LINKER,\"*\");return this.addToChain(e,d,true),d}let{symbol:t,isInlineSmiles:n,rawPayload:o,inlineSource:r,span:s}=this.consumeMonomerSymbol(false),a=this.makeAtom(e,b.LINKER,t);return r!==void 0&&(a.inlineSource=r),n&&this.registerInlineSmiles(o,s,v.RNA),this.addToChain(e,a,true),a}parseRnaAlternation(e,t){let n=e.backboneAtoms.length;if(this.cursor.advance(),this.looksLikeFlatAlternation()){let r=[],s=null;for(;!this.cursor.at(\"rparen\")&&!this.cursor.isAtEnd();)if(r.push(this.parseAlternationCandidate(v.RNA)),this.cursor.at(\"comma\"))s=\"or\",this.cursor.advance();else if(this.cursor.at(\"plus\"))s=\"and\",this.cursor.advance();else break;this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' in RNA alternation\",this.cursor.currentSpan());let a=s===\"and\"?\"+\":\",\",l=`(${r.map(u=>u.symbol+(u.ratio!==void 0?`:${String(u.ratio)}`:\"\")).join(a)})`,d=this.makeAtom(e,b.BASE,\"?\");d.bio.ambiguity=l,d.bio.ambiguityKind=s===\"and\"?\"and\":\"or\",this.addToChain(e,d,true);let c=e.backboneAtoms[e.backboneAtoms.length-2];c!==void 0&&this.addBond(e,c,d,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1}),this.maybeRepeatBracket(e,[d]),this.maybeAttachAnnotation(e);return}for(this.parseRnaItem(e,t);this.cursor.at(\"dot\")&&(this.cursor.advance(),!(this.cursor.at(\"rparen\")||this.cursor.isAtEnd()));)this.parseRnaItem(e,t);this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' in RNA repeat\",this.cursor.currentSpan());let o=e.backboneAtoms.slice(n);this.maybeRepeatBracket(e,o),this.maybeAttachAnnotation(e);}looksLikeFlatAlternation(){let e=1,t=0,n=false;for(;;){let o=this.cursor.peek(t);if(o.kind===\"eof\")return n;if(o.kind===\"rparen\"){if(e-=1,e===0)return n}else {if(o.kind===\"lparen\")return  false;if(o.kind===\"dot\")return  false;e===1&&(o.kind===\"comma\"||o.kind===\"plus\")&&(n=true);}if(t+=1,t>256)return n}}parseChemBody(e){let t;if(this.cursor.at(\"asterisk\"))this.cursor.advance(),t=this.makeAtom(e,b.CHEM,\"*\"),this.addToChain(e,t,true);else {let{symbol:n,isInlineSmiles:o,rawPayload:r,inlineSource:s,span:a}=this.consumeMonomerSymbol(false);t=this.makeAtom(e,b.CHEM,n),s!==void 0&&(t.inlineSource=s),o&&this.registerInlineSmiles(r,a,v.CHEM),this.addToChain(e,t,true);}this.maybeAttachAnnotation(e),this.cursor.at(\"apos\")&&this.maybeRepeatBracket(e,[t]),this.cursor.at(\"rbrace\")||(this.emit(\"error\",\"chem-multiple-monomers\",`CHEM polymer '${e.id}' must contain exactly one monomer`,this.cursor.currentSpan()),this.skipUntil([\"rbrace\",\"eof\"]));}parseBlobBody(e){let t,n,o=false,r=\"\",s,a=this.cursor.currentSpan();if(this.cursor.at(\"inline-smiles\")){let d=this.cursor.advance();o=Ce(d.value),r=d.value,t=d.value,n=d.value,s=d.value,a=d.span;}else if(this.cursor.at(\"identifier\")){let d=this.cursor.advance();t=d.value,n=d.value,a=d.span;}else this.emit(\"error\",\"unknown-blobtype\",\"Expected BLOB identifier\",this.cursor.currentSpan()),t=\"?\",n=\"?\";let l=this.makeAtom(e,b.BLOB,t);l.bio.blobtype=n,s!==void 0&&(l.inlineSource=s),o&&this.registerInlineSmiles(r,a,v.BLOB),this.addToChain(e,l,true),this.maybeAttachAnnotation(e);}parseGroupBody(e){let t=0;for(;;){let n=this.cursor.peek();if(n.kind===\"eof\"||t===0&&n.kind===\"rbrace\")break;n.kind===\"lbrace\"&&(t+=1),n.kind===\"rbrace\"&&(t-=1),this.cursor.advance();}}parseConnections(){if(!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()))for(this.parseConnection();this.cursor.at(\"pipe\")&&(this.cursor.advance(),!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()));)this.parseConnection();}parseConnection(){let e=this.cursor.currentSpan(),t=this.cursor.optional(\"identifier\");if(t===null){this.emit(\"error\",\"unexpected-token\",\"Expected chain id in connection\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}if(this.cursor.optional(\"comma\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected ',' in connection\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let n=this.cursor.optional(\"identifier\");if(n===null){this.emit(\"error\",\"unexpected-token\",\"Expected second chain id in connection\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}if(this.cursor.optional(\"comma\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected ',' before connection position\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let o=this.parsePosition();if(this.cursor.optional(\"colon\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected ':' between position and R-group\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let r=this.parseRGroupSpec();if(this.cursor.optional(\"dash\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected '-' between connection endpoints\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let s=this.parsePosition();if(this.cursor.optional(\"colon\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected ':' before second R-group\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let a=this.parseRGroupSpec(),l=this.cursor.optional(\"quote-string\"),d=r.kind===\"pair\"&&a.kind===\"pair\"?\"hbond\":\"cross-polymer\",c={chain1:t.value,pos1:o,r1:r,chain2:n.value,pos2:s,r2:a,kind:d,span:{start:e.start,end:l?.span.end??this.cursor.peek().span.start},...l!==null?{tag:l.value}:{}};this.pendingBonds.push(c);}parsePosition(){let e=this.cursor.peek();return e.kind===\"integer\"?(this.cursor.advance(),{kind:\"index\",value:parseInt(e.value,10)}):e.kind===\"question\"?(this.cursor.advance(),{kind:\"any\"}):e.kind===\"identifier\"?(this.cursor.advance(),this.emit(\"info\",\"symbol-position-reference\",`Connection position uses monomer symbol '${e.value}' as chain-level ambiguity`,e.span),{kind:\"symbol\",value:e.value}):(this.emit(\"error\",\"invalid-position\",`Expected position (integer, '?', or symbol), got '${e.value}'`,e.span),{kind:\"any\"})}parseRGroupSpec(){let e=this.cursor.peek();if(e.kind===\"question\")return this.cursor.advance(),{kind:\"unspecified\"};if(e.kind===\"asterisk\")return this.cursor.advance(),{kind:\"wildcard\"};if(e.kind===\"identifier\"){if(this.cursor.advance(),e.value===\"pair\")return {kind:\"pair\"};let t=/^R([1-9][0-9]*)$/.exec(e.value);return t===null?(this.emit(\"error\",\"invalid-rgroup\",`Expected R-group label, got '${e.value}'`,e.span),{kind:\"unspecified\"}):{kind:\"numeric\",r:parseInt(t[1],10)}}return this.emit(\"error\",\"invalid-rgroup\",`Expected R-group label, got '${e.value}'`,e.span),{kind:\"unspecified\"}}parseGroupsSection(){if(!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()))for(this.parseGroupOrBondRatio();this.cursor.at(\"pipe\")&&(this.cursor.advance(),!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()));)this.parseGroupOrBondRatio();}parseGroupOrBondRatio(){let e=this.cursor.optional(\"identifier\");if(e===null){this.emit(\"error\",\"unexpected-token\",\"Expected group or bond-ratio identifier\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}this.cursor.at(\"lparen\")?this.parseGroupAfterId(e):this.cursor.at(\"plus\")?this.parseBondRatioAfterId(e):(this.emit(\"warning\",\"unexpected-token\",`Expected '(' or '+' after id '${e.value}' in section 3`,this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]));}parseGroupAfterId(e){let t=lo(e.value);(t===null||!t.isGroup)&&this.emit(\"error\",\"unknown-group-reference\",`Group id must be 'G<n>', got '${e.value}'`,e.span),this.cursor.advance();let n=[],o=\"or\",r=null;for(;!this.cursor.at(\"rparen\")&&!this.cursor.isAtEnd();){let s=this.parseGroupMember();if(s!==null&&n.push(s),this.cursor.at(\"comma\"))r===null&&(r=\"or\",o=\"or\"),this.cursor.advance();else if(this.cursor.at(\"plus\"))r===null&&(r=\"and\",o=\"and\"),this.cursor.advance();else break}this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' to close group\",this.cursor.currentSpan()),this.groups.push({id:e.value,kind:o,members:n});}parseGroupMember(){let e=this.cursor.optional(\"identifier\");if(e===null)return this.emit(\"error\",\"unexpected-token\",\"Expected group member id\",this.cursor.currentSpan()),null;let t;return this.cursor.optional(\"colon\")!==null&&(t=this.parseRatio()),t===void 0?{target:e.value}:{target:e.value,ratio:t}}parseRatio(){let e=this.cursor.peek();if(e.kind===\"integer\"||e.kind===\"decimal\"){this.cursor.advance();let t=parseFloat(e.value);if(this.cursor.at(\"dash\")){this.cursor.peek();if(this.cursor.peek(1).kind===\"integer\"){this.cursor.advance();let o=this.cursor.advance();this.emit(\"info\",\"ratio-range\",`Ratio range ${e.value}-${o.value}; using lower bound`,{start:e.span.start,end:o.span.end});}}return t}return e.kind===\"question\"?(this.cursor.advance(),\"?\"):(this.emit(\"error\",\"unexpected-token\",`Expected ratio after ':', got '${e.value}'`,e.span),0)}parseBondRatioAfterId(e){this.cursor.advance();let t=this.cursor.optional(\"identifier\");if(t===null){this.emit(\"error\",\"unexpected-token\",\"Expected second chain id in bond-ratio\",this.cursor.currentSpan());return}let n;if(this.cursor.optional(\"colon\")!==null){let r=this.parseRatio();typeof r==\"number\"&&(n=r);}let o=this.pendingBonds.find(r=>r.chain1===e.value&&r.chain2===t.value||r.chain1===t.value&&r.chain2===e.value);if(o===void 0){this.emit(\"warning\",\"bond-ratio-no-matching-bond\",`Bond-ratio for ${e.value}+${t.value} has no matching cross-polymer bond`,e.span);return}n!==void 0&&(o.ratio={numerator:n});}parseAnnotationsSection(){if(this.cursor.at(\"dollar\")||this.cursor.isAtEnd())return;this.cursor.position();if(this.cursor.at(\"lbrace\")){this.parseAnnotation20(),this.cursor.at(\"pipe\")&&(this.emit(\"info\",\"annotation-mixed-versions\",\"Mixed HELM 2.0 JSON and HELM 1.0 pipe annotations\",this.cursor.currentSpan()),this.cursor.advance(),this.parseAnnotation10Entries());return}this.parseAnnotation10Entries();}parseAnnotation20(){let e=this.cursor.currentSpan(),t=0,n=e.end;for(;!this.cursor.isAtEnd();){let s=this.cursor.peek();if(s.kind===\"lbrace\")t+=1;else if(s.kind===\"rbrace\"&&(t-=1,t===0)){n=s.span.end,this.cursor.advance();break}this.cursor.advance();}let o=this.source.slice(e.start,n),r=null;try{r=JSON.parse(o);}catch{this.emit(\"warning\",\"annotation-malformed-json\",\"Annotation block is not valid JSON\",{start:e.start,end:n}),this.annotations={perPolymer:this.annotations.perPolymer,version:this.annotations.version,raw:o};return}if(r!==null&&typeof r==\"object\"&&!Array.isArray(r)){let s=new Map(this.annotations.perPolymer);for(let[a,l]of Object.entries(r))l!==null&&typeof l==\"object\"&&!Array.isArray(l)?(s.set(a,{...l}),this.chainById.has(a)||this.emit(\"warning\",\"annotation-unknown-polymer\",`Annotation references unknown polymer '${a}'`,e)):s.set(a,{value:l});this.annotations={perPolymer:s,version:this.annotations.version};}else this.emit(\"warning\",\"annotation-malformed-json\",\"Annotation block parsed but is not an object\",{start:e.start,end:n}),this.annotations={perPolymer:this.annotations.perPolymer,version:this.annotations.version,raw:o};}parseAnnotation10Entries(){for(this.parseAnnotation10One();this.cursor.at(\"pipe\")&&(this.cursor.advance(),!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()));)this.parseAnnotation10One();}parseAnnotation10One(){let e=this.cursor.optional(\"identifier\");if(e===null){this.emit(\"warning\",\"annotation-malformed-json\",\"Expected polymer-id in HELM 1.0 annotation\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}if(this.cursor.optional(\"lbrace\")===null){this.emit(\"warning\",\"annotation-malformed-json\",\"Expected '{' after polymer-id\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let t=[];for(;!this.cursor.at(\"rbrace\")&&!this.cursor.isAtEnd();)t.push(this.cursor.advance().value);if(this.cursor.optional(\"rbrace\")===null){this.emit(\"error\",\"unterminated-brace\",\"Expected '}' to close annotation\",this.cursor.currentSpan());return}let n=t.join(\"\").trim(),o=new Map(this.annotations.perPolymer),r=o.get(e.value)??{};n===\"ss\"||n===\"as\"?o.set(e.value,{...r,strandtype:n}):o.set(e.value,{...r,[n]:true}),this.chainById.has(e.value)||this.emit(\"warning\",\"annotation-unknown-polymer\",`Annotation references unknown polymer '${e.value}'`,e.span),this.annotations={perPolymer:o,version:this.annotations.version};}parseVersionTrailer(){let e=this.cursor.optional(\"identifier\");if(e===null){this.annotations={...this.annotations,version:\"\"};return}let t=e.value;if(this.cursor.at(\"dot\")&&this.cursor.peek(1).kind===\"integer\"){this.cursor.advance();let n=this.cursor.advance();t=`${e.value}.${n.value}`;}this.annotations={...this.annotations,version:t};}skipUntil(e){for(;!this.cursor.isAtEnd();){if(e.includes(this.cursor.peek().kind))return;this.cursor.advance();}}consumeMonomerSymbol(e){let t=this.cursor.peek();if(t.kind===\"inline-smiles\"){this.cursor.advance();let n=Ce(t.value);return {symbol:t.value,isInlineSmiles:n,rawPayload:t.value,inlineSource:t.value,span:t.span}}if(t.kind===\"identifier\"){this.cursor.advance();let n=t.value,o=t.span;for(;this.cursor.peek().kind===\"dash\"&&this.cursor.peek(1).kind===\"integer\"&&(this.cursor.peek(2).kind===\"identifier\"||this.cursor.peek(2).kind===\"dash\");){this.cursor.advance();let s=this.cursor.advance();if(n=`${n}-${s.value}`,o=s.span,this.cursor.peek().kind===\"identifier\"){let a=this.cursor.advance();n=`${n}${a.value}`,o=a.span;}}return {symbol:n,isInlineSmiles:false,rawPayload:n,span:{start:t.span.start,end:o.end}}}if(t.kind===\"asterisk\"||t.kind===\"underscore\"||t.kind===\"question\")return this.cursor.advance(),{symbol:t.value,isInlineSmiles:false,rawPayload:t.value,span:t.span};if(t.kind===\"integer\"&&this.cursor.peek(1).kind===\"identifier\"){let n=this.cursor.advance(),o=this.cursor.advance(),r=`${n.value}${o.value}`;return {symbol:r,isInlineSmiles:false,rawPayload:r,span:{start:n.span.start,end:o.span.end}}}return this.emit(\"error\",\"unexpected-token\",`Expected monomer symbol, got '${t.value}'`,t.span),{symbol:\"?\",isInlineSmiles:false,rawPayload:\"\",span:t.span}}maybeRepeatBracket(e,t){if(!this.cursor.at(\"apos\"))return;let n=this.cursor.currentSpan();this.cursor.advance();let o=this.cursor.optional(\"integer\");if(o===null){this.emit(\"error\",\"unexpected-token\",\"Expected integer in repeat bracket\",this.cursor.currentSpan()),this.cursor.optional(\"apos\");return}let r=parseInt(o.value,10),s=r;if(this.cursor.at(\"dash\")){this.cursor.advance();let a=this.cursor.optional(\"integer\");a===null?this.emit(\"error\",\"unexpected-token\",\"Expected integer after '-' in repeat bracket\",this.cursor.currentSpan()):s=parseInt(a.value,10);}if(this.cursor.optional(\"apos\")===null&&this.emit(\"error\",\"unterminated-apostrophe\",\"Expected closing apostrophe\",this.cursor.currentSpan()),t.length===0){this.emit(\"warning\",\"repeat-on-empty-bracket\",\"Repeat bracket applied to empty content\",n);return}if(s<r){this.emit(\"warning\",\"repeat-range-inverted\",`Repeat range ${r}-${s} has max < min; swapping`,n);let a=r;r=s,s=a;}if(r===0&&s===0){this.emit(\"warning\",\"repeat-zero-count\",\"Repeat bracket with zero count\",n);return}s>1e4&&this.emit(\"warning\",\"bracket-repeat-too-large\",`Repeat range upper bound ${s} > 10000`,n),e.polymerType===v.CHEM&&this.emit(\"error\",\"repeat-on-non-iterable-polymer\",`Repeat bracket not allowed on CHEM polymer '${e.id}'`,n),this.groups.push({id:`${e.id}/bracket@${t[0]?.id??0}`,kind:\"bracket\",members:t.map(a=>({target:String(a.id)})),repeat:{min:r,max:s}});}maybeAttachAnnotation(e){let t=e.backboneAtoms[e.backboneAtoms.length-1];t!==void 0&&this.maybeAttachAnnotationTo(t);}maybeAttachAnnotationTo(e){if(e===void 0)return;let t=this.cursor.optional(\"quote-string\");t!==null&&(e.tag=t.value);}registerInlineSmiles(e,t,n){if(Ce(e)){if(this.lib===null){this.emit(\"info\",\"inline-smiles-no-lib\",\"Inline SMILES seen but no monomer library available for registration\",t);return}try{this.lib.addMonomer;let o=this.lib.registerInlineSmilesMonomer;typeof o==\"function\"&&o.call(this.lib,n,e);}catch(o){let r=o instanceof Error?o.message:String(o);this.emit(\"warning\",\"inline-smiles-without-r-groups\",`Inline SMILES registration failed: ${r}`,t);}}}makeAtom(e,t,n){return {id:this.atomIds.next(),p:{x:0,y:0},biotype:t,symbol:n,monomer:null,bio:{chainId:e.id,positionInChain:0,continuousId:0},hidden:false,selected:false,highlighted:false}}addToChain(e,t,n){e.allAtoms.push(t),n&&(e.backboneAtoms.push(t),t.bio.positionInChain=e.backboneAtoms.length);}addBond(e,t,n,o,r,s){let a=this.bondIds.next();e.bonds.push({id:a,a1:t,a2:n,kind:o,r1:r,r2:s});}finalize(){let e=[];for(let a of this.pendingBonds){let l=this.chainById.get(a.chain1),d=this.chainById.get(a.chain2);if(l===void 0){this.emit(\"error\",\"unknown-chain-reference\",`Connection references unknown chain '${a.chain1}'`,a.span);continue}if(d===void 0){this.emit(\"error\",\"unknown-chain-reference\",`Connection references unknown chain '${a.chain2}'`,a.span);continue}let c=this.resolveAtomByPosition(l,a.pos1,a.span),u=this.resolveAtomByPosition(d,a.pos2,a.span);if(c===null||u===null)continue;a.r1.kind===\"pair\"&&c.branchAtom!==void 0&&(c=c.branchAtom),a.r2.kind===\"pair\"&&u.branchAtom!==void 0&&(u=u.branchAtom);let p={id:this.bondIds.next(),a1:c,a2:u,kind:a.kind,r1:a.r1,r2:a.r2,...a.tag!==void 0?{tag:a.tag}:{},...a.ratio!==void 0?{ratio:a.ratio}:{}};e.push(p);}let t=[],n=[],o=[];for(let a of this.chains){for(let u of a.allAtoms)t.push(u);for(let u of a.bonds)n.push(u);let l=this.annotations.perPolymer.get(a.id),d=l===void 0?void 0:l.strandtype,c=d===\"ss\"||d===\"as\"?d:void 0;o.push({id:a.id,polymerType:a.polymerType,backboneAtoms:a.backboneAtoms,bonds:a.bonds,...a.annotation!==void 0?{annotation:a.annotation}:{},...c!==void 0?{strandType:c}:{}});}for(let a of e)n.push(a);let r=0;for(let a of this.chains)for(let l of a.backboneAtoms)r+=1,l.bio.continuousId=r,l.branchAtom!==void 0&&(r+=1,l.branchAtom.bio.continuousId=r);let s=[];for(let a of this.groups)s.push({id:a.id,kind:a.kind,members:a.members,...a.repeat!==void 0?{repeat:a.repeat}:{}});return {atoms:t,bonds:n,chains:o,groups:s,annotations:this.annotations}}sourceOrderAtoms(e){let t=[];for(let n of e.backboneAtoms)t.push(n),n.branchAtom!==void 0&&t.push(n.branchAtom);return t}resolveAtomByPosition(e,t,n){if(t.kind===\"any\")return e.backboneAtoms[0]??null;if(t.kind===\"symbol\"){let s=e.backboneAtoms.find(a=>a.symbol===t.value);if(s===void 0){let a=e.allAtoms.find(l=>l.symbol===t.value);return a===void 0?(this.emit(\"warning\",\"position-out-of-range\",`Chain '${e.id}' has no monomer with symbol '${t.value}'`,n),e.backboneAtoms[0]??null):a}return s}let o=this.sourceOrderAtoms(e),r=t.value;return r<1||r>o.length?(this.emit(\"error\",\"position-out-of-range\",`Position ${r} out of range for chain '${e.id}' (length ${o.length})`,n),e.backboneAtoms[0]??null):o[r-1]}emit(e,t,n,o){let r={severity:e,code:t,message:n,...o!==void 0?{span:{start:o.start,end:o.end}}:{}};if(this.diagnostics.push(r),this.mode===\"strict\"&&e===\"error\")throw new N(t,n,{...o!==void 0?{span:{start:o.start,end:o.end}}:{}})}};function uo(i,e,t){for(let n of t){if(n.kind!==\"backbone\"||n.r1.kind!==\"numeric\"||n.r2.kind!==\"numeric\")continue;let o=n.a1.id===i.id&&n.a2.id===e.id&&n.r1.r===2&&n.r2.r===1,r=n.a1.id===e.id&&n.a2.id===i.id&&n.r1.r===2&&n.r2.r===1;if(o||r)return  true}return  false}function fr(i){let e=false;for(let c of i.chains){for(let u=0;u<c.backboneAtoms.length-1;u++){let m=c.backboneAtoms[u],p=c.backboneAtoms[u+1];if(!uo(m,p,i.bonds)){e=true;break}}if(e)break}if(!e)return i;let t=new Set(i.chains.map(c=>c.id)),n=c=>{let u=1;for(;t.has(`${c}${u}`);)u+=1;let m=`${c}${u}`;return t.add(m),m},o=[];for(let c of i.chains){let u=[[]],m=u[0];for(let p=0;p<c.backboneAtoms.length;p++){let h=c.backboneAtoms[p];if(m.push(h),p<c.backboneAtoms.length-1){let f=c.backboneAtoms[p+1];uo(h,f,i.bonds)||(m=[],u.push(m));}}for(let p=0;p<u.length;p++){let f={id:p===0?c.id:n(c.polymerType),polymerType:c.polymerType,atoms:u[p]};p===0&&c.annotation!==void 0&&(f.annotation=c.annotation),o.push(f);}}let r=new Map;for(let c of o)for(let u=0;u<c.atoms.length;u++){let m=c.atoms[u];r.set(m.id,{chainId:c.id,pos:u+1}),m.branchAtom!==void 0&&r.set(m.branchAtom.id,{chainId:c.id,pos:u+1});}let s=new Map;for(let c of i.atoms){let u=r.get(c.id);if(u===void 0){s.set(c.id,c);continue}if(c.bio.chainId===u.chainId&&c.bio.positionInChain===u.pos){s.set(c.id,c);continue}s.set(c.id,{...c,bio:{...c.bio,chainId:u.chainId,positionInChain:u.pos}});}for(let c of i.atoms){if(c.branchAtom===void 0)continue;let u=s.get(c.id),m=s.get(c.branchAtom.id);u===void 0||m===void 0||(u.branchAtom=m);}let a=i.bonds.map(c=>{let u=s.get(c.a1.id)??c.a1,m=s.get(c.a2.id)??c.a2;return u===c.a1&&m===c.a2?c:{...c,a1:u,a2:m}}),l=o.map(c=>{let u=c.atoms.map(f=>s.get(f.id)??f),m=new Set;for(let f of c.atoms)m.add(f.id),f.branchAtom!==void 0&&m.add(f.branchAtom.id);let p=[];for(let f of a)m.has(f.a1.id)&&m.has(f.a2.id)&&p.push(f);return {id:c.id,polymerType:c.polymerType,backboneAtoms:u,bonds:p,...c.annotation!==void 0?{annotation:c.annotation}:{}}});return {atoms:i.atoms.map(c=>s.get(c.id)??c),bonds:a,chains:l,groups:i.groups,annotations:i.annotations}}function Re(i,e){let t=fr(i);return new pn(t,e??{}).emit()}var pn=class{constructor(e,t){this.mol=e,this.options=t;}emit(){let t=this.orderedChains().map(a=>this.emitPolymer(a)).join(\"|\"),n=this.emitConnections(),o=this.emitGroupsAndBondRatios(),r=this.emitAnnotations(),s=this.versionTrailer();return `${t}$${n}$${o}$${r}${s}`}orderedChains(){if(this.options.canonicalize!==true)return this.mol.chains;let e=this.mol.chains.slice();return e.sort((t,n)=>t.polymerType!==n.polymerType?t.polymerType<n.polymerType?-1:1:t.id<n.id?-1:t.id>n.id?1:0),e}emitPolymer(e){let t=this.emitChainBody(e),n=e.annotation!==void 0?`\"${te(e.annotation)}\"`:\"\";return `${e.id}{${t}}${n}`}emitChainBody(e){switch(e.polymerType){case \"PEPTIDE\":return this.emitPeptideBody(e);case \"RNA\":return this.emitRnaBody(e);case \"CHEM\":return this.emitChemBody(e);case \"BLOB\":return this.emitBlobBody(e);default:return \"\"}}emitPeptideBody(e){let t=this.bracketsForChain(e.id),n=[],o=0,r=0,s=null;for(;o<e.backboneAtoms.length;){let a=e.backboneAtoms[o],l=t.find(c=>c.startAtomId===a.id);l!==void 0&&s===null&&(n.push(\"(\"),s=l,r+=1),n.push(this.emitMonomerToken(a));let d=a.tag!==void 0?`\"${te(a.tag)}\"`:\"\";n.push(d),s!==null&&s.endAtomId===a.id&&(n.push(`)${mo(s.min,s.max)}`),s=null,r-=1),o+=1,o<e.backboneAtoms.length&&n.push(\".\");}return n.join(\"\")}emitRnaBody(e){let t=this.bracketsForChain(e.id),n=[],o=0,r=true,s=null,a=d=>{s!==null&&s.endAtomId===d&&(n.push(`)${mo(s.min,s.max)}`),s=null);},l=d=>{let c=t.find(u=>u.startAtomId===d);c!==void 0&&s===null&&(n.push(\"(\"),s=c);};for(;o<e.backboneAtoms.length;){let d=e.backboneAtoms[o];if(r||n.push(\".\"),r=false,d.biotype===b.NUCLEOTIDE){l(d.id),n.push(this.emitMonomerToken(d)),d.tag!==void 0&&n.push(`\"${te(d.tag)}\"`),a(d.id),o+=1;continue}if(d.biotype===b.SUGAR){l(d.id),n.push(this.emitMonomerToken(d)),d.tag!==void 0&&n.push(`\"${te(d.tag)}\"`),d.branchAtom!==void 0&&(n.push(\"(\"),n.push(this.emitMonomerToken(d.branchAtom)),d.branchAtom.tag!==void 0&&n.push(`\"${te(d.branchAtom.tag)}\"`),n.push(\")\"));let c=e.backboneAtoms[o+1];c!==void 0&&c.biotype===b.LINKER?(n.push(this.emitMonomerToken(c)),c.tag!==void 0&&n.push(`\"${te(c.tag)}\"`),a(c.id),o+=2):(a(d.id),o+=1);continue}l(d.id),n.push(this.emitMonomerToken(d)),d.tag!==void 0&&n.push(`\"${te(d.tag)}\"`),a(d.id),o+=1;}return n.join(\"\")}emitChemBody(e){let t=e.backboneAtoms[0];if(t===void 0)return \"\";let n=t.tag!==void 0?`\"${te(t.tag)}\"`:\"\";return `${this.emitMonomerToken(t)}${n}`}emitBlobBody(e){let t=e.backboneAtoms[0];if(t===void 0)return \"\";let n=t.tag!==void 0?`\"${te(t.tag)}\"`:\"\";return `${this.emitMonomerToken(t)}${n}`}emitMonomerToken(e){let t;return e.inlineSource!==void 0?t=`[${e.inlineSource}]`:e.bio.ambiguity!==void 0&&(e.symbol===\"?\"||e.bio.ambiguity.startsWith(\"(\"))?t=e.bio.ambiguity:t=e.symbol,this.options.includeHighlights===true&&e.selected?`<span style='background:#bbf;'>${t}</span>`:t}emitConnections(){let e=[];for(let t of this.crossPolymerBonds())e.push(this.emitConnection(t));return e.join(\"|\")}*crossPolymerBonds(){let e=new Map;for(let t of this.mol.chains){let n=new Map;for(let o=0;o<t.backboneAtoms.length;o++)n.set(t.backboneAtoms[o].id,o);e.set(t.id,n);}for(let t of this.mol.bonds){if(t.kind===\"backbone\"){if(t.a1.bio.chainId===t.a2.bio.chainId){let n=e.get(t.a1.bio.chainId);if(n!==void 0){let o=n.get(t.a1.id),r=n.get(t.a2.id);if(o!==void 0&&r!==void 0&&Math.abs(o-r)===1)continue}}yield t;continue}if(t.kind===\"branch\"){if(t.a1.branchAtom!==void 0&&t.a1.branchAtom.id===t.a2.id||t.a2.branchAtom!==void 0&&t.a2.branchAtom.id===t.a1.id)continue;yield t;continue}yield t;}}emitConnection(e){let t=po(e.r1,e.kind),n=po(e.r2,e.kind),o=e.tag!==void 0?`\"${te(e.tag)}\"`:\"\",r=String(this.connectionPosition(e.a1)),s=String(this.connectionPosition(e.a2));return `${e.a1.bio.chainId},${e.a2.bio.chainId},${r}:${t}-${s}:${n}${o}`}connectionPosition(e){return le(e,this.mol.chains.find(t=>t.id===e.bio.chainId))}emitGroupsAndBondRatios(){let e=[];for(let t of this.mol.groups)t.kind!==\"bracket\"&&e.push(this.emitGroup(t));for(let t of this.mol.bonds){if(t.kind!==\"cross-polymer\"||t.ratio===void 0)continue;let n=t.ratio.denominator!==void 0?`${t.ratio.numerator}/${t.ratio.denominator}`:`${t.ratio.numerator}`;e.push(`${t.a1.bio.chainId}+${t.a2.bio.chainId}:${n}`);}return e.join(\"|\")}emitGroup(e){let t=e.kind===\"and\"?\"+\":\",\",n=e.members.map(o=>br(o)).join(t);return `${e.id}(${n})`}emitAnnotations(){let e=this.mol.annotations.perPolymer;if(e.size===0)return \"\";let t={};for(let[n,o]of e)t[n]=o;return JSON.stringify(t)}versionTrailer(){let e=this.options.version??\"V2.0\";if(e===\"none\")return \"\";if(e===\"preserve\"){let t=this.mol.annotations.version;return t===\"\"?\"\":`$${t}`}return `$${e}`}bracketsForChain(e){let t=[],n=new Map;for(let o of this.mol.atoms)n.set(o.id,o.bio.chainId);for(let o of this.mol.groups){if(o.kind!==\"bracket\")continue;let r=[];for(let l of o.members){let d=parseInt(l.target,10);Number.isFinite(d)&&r.push(d);}if(r.length===0)continue;let s=new Set;for(let l of r){let d=n.get(l);d!==void 0&&s.add(d);}if(!s.has(e)||s.size>1)continue;let a=o.repeat??{min:1,max:1};t.push({members:r,min:a.min,max:a.max,set:new Set(r),startAtomId:r[0],endAtomId:r[r.length-1]});}return t}};function te(i){let e=\"\";for(let t=0;t<i.length;t++){let n=i.charCodeAt(t);if(n===34){e+='\\\\\"';continue}if(n===92){e+=\"\\\\\\\\\";continue}if(n===10){e+=\"\\\\n\";continue}if(n===13){e+=\"\\\\r\";continue}if(n===9){e+=\"\\\\t\";continue}e+=i.charAt(t);}return e}function mo(i,e){return i===e?`'${i}'`:`'${i}-${e}'`}function po(i,e){switch(i.kind){case \"numeric\":return `R${i.r}`;case \"unspecified\":return \"?\";case \"wildcard\":return \"*\";case \"pair\":return \"pair\";case \"positional\":return `${i.position}:R${i.r}`;default:return \"?\"}}function br(i){return i.ratio===void 0?i.target:`${i.target}:${i.ratio}`}function fn(i){return new hn(i).run()}var hn=class{constructor(e){this.chainIdMap=new Map;this.mol=e;}run(){let e=this.mol.chains.slice().sort((m,p)=>m.polymerType!==p.polymerType?m.polymerType<p.polymerType?-1:1:fo(m.id,p.id)),t={},n=[];for(let m of e){let p=yr(m.polymerType);t[p]=(t[p]??0)+1;let h=`${p}${t[p]}`;this.chainIdMap.set(m.id,h),n.push(m);}let o=new Map;for(let m of this.mol.atoms){let p=this.chainIdMap.get(m.bio.chainId)??m.bio.chainId;o.set(m.id,{...m,bio:{...m.bio,chainId:p}});}for(let m of this.mol.atoms){if(m.branchAtom===void 0)continue;let p=o.get(m.id),h=o.get(m.branchAtom.id);p!==void 0&&h!==void 0&&(p.branchAtom=h);}let r=this.mol.bonds.map(m=>({...m,a1:o.get(m.a1.id)??m.a1,a2:o.get(m.a2.id)??m.a2})),s=new Map;for(let m of r)s.set(m.id,m);let a=n.map(m=>{let p=this.chainIdMap.get(m.id)??m.id,h=[];for(let y of m.backboneAtoms){let w=o.get(y.id);w!==void 0&&h.push(w);}let f=[];for(let y of m.bonds){let w=s.get(y.id);w!==void 0&&f.push(w);}return {id:p,polymerType:m.polymerType,backboneAtoms:h,bonds:f,...m.annotation!==void 0&&m.annotation.length>0?{annotation:m.annotation}:{}}}),l=new Map;for(let m of a)l.set(m.id,m);r.sort((m,p)=>{let h=ho(m.kind),f=ho(p.kind);if(h&&!f)return 1;if(!h&&f)return  -1;if(!h&&!f)return m.id-p.id;let y=m.a1.bio.chainId,w=p.a1.bio.chainId;if(y!==w)return y<w?-1:1;let _=m.a2.bio.chainId,M=p.a2.bio.chainId;if(_!==M)return _<M?-1:1;let k=le(m.a1,l.get(m.a1.bio.chainId)),x=le(p.a1,l.get(p.a1.bio.chainId));if(k!==x)return k-x;let T=le(m.a2,l.get(m.a2.bio.chainId)),E=le(p.a2,l.get(p.a2.bio.chainId));return T-E});let d=this.renumberGroups(this.mol.groups),c=this.rekeyAnnotations(this.mol.annotations);return {atoms:this.mol.atoms.map(m=>o.get(m.id)),bonds:r,chains:a,groups:d,annotations:c}}renumberGroups(e){let t=[],n=[];for(let r of e)r.kind===\"bracket\"?t.push(this.rekeyBracket(r)):n.push(r);n.sort((r,s)=>fo(r.id,s.id));let o={G:0};return n.map(r=>{o.G+=1;let s=`G${o.G}`;return {...r,id:s,members:r.members.map(a=>this.rekeyMember(a))}}).concat(t)}rekeyBracket(e){return e}rekeyMember(e){let t=this.chainIdMap.get(e.target);return t===void 0?e:e.ratio===void 0?{target:t}:{target:t,ratio:e.ratio}}rekeyAnnotations(e){let t=new Map;for(let[n,o]of e.perPolymer){let r=this.chainIdMap.get(n)??n;Object.keys(o).length!==0&&t.set(r,o);}return {perPolymer:t,version:e.version}}};function yr(i){switch(i){case \"PEPTIDE\":return \"PEPTIDE\";case \"RNA\":return \"RNA\";case \"CHEM\":return \"CHEM\";case \"BLOB\":return \"BLOB\";default:return \"BLOB\"}}function ho(i){return i===\"cross-polymer\"||i===\"hbond\"}function fo(i,e){let t=/^([A-Z]+)([0-9]+)$/.exec(i),n=/^([A-Z]+)([0-9]+)$/.exec(e);return t===null||n===null?i<e?-1:i>e?1:0:t[1]!==n[1]?t[1]<n[1]?-1:1:parseInt(t[2],10)-parseInt(n[2],10)}function bo(i){let e=Ee(i),t=new Map;for(let a of i.atoms){let l=e.get(a.id);if(l===void 0||l===a.bio.continuousId){t.set(a.id,a);continue}t.set(a.id,{...a,bio:{...a.bio,continuousId:l}});}for(let a of i.atoms){if(a.branchAtom===void 0)continue;let l=t.get(a.id),d=t.get(a.branchAtom.id);l===void 0||d===void 0||(l.branchAtom=d);}let n=i.bonds.map(a=>{let l=t.get(a.a1.id),d=t.get(a.a2.id);return l===void 0||d===void 0||l===a.a1&&d===a.a2?a:{...a,a1:l,a2:d}}),o=new Map;for(let a of n)o.set(a.id,a);let r=i.chains.map(a=>{let l=[];for(let c of a.backboneAtoms){let u=t.get(c.id);l.push(u??c);}let d=[];for(let c of a.bonds){let u=o.get(c.id);d.push(u??c);}return {id:a.id,polymerType:a.polymerType,backboneAtoms:l,bonds:d,...a.annotation!==void 0?{annotation:a.annotation}:{}}});return {atoms:i.atoms.map(a=>t.get(a.id)??a),bonds:n,chains:r,groups:i.groups,annotations:i.annotations}}function bn(i,e){let n=et(i,e??null,{mode:\"lenient\",resolveMonomers:false}),o=gr(n.mol),r=bo(o.mol),s=new Map;for(let d of r.atoms)s.set(d.id,d.bio.continuousId);let a=new Map;for(let[d,c]of o.survivorByOldContinuousId){let u=s.get(c);u!==void 0&&a.set(d,u);}let l=Re(r,{version:\"V2.0\"});return {srcHelm:i,resHelm:l,monomerMap:a}}function gr(i){let e=new Map;for(let u of i.atoms)e.set(u.bio.continuousId,u.id);let t=new Set;for(let u of i.atoms)u.symbol===\"*\"&&t.add(u.id);if(t.size===0)return {mol:i,survivorByOldContinuousId:e};let n=new Map;for(let u of i.atoms)n.set(u.id,[]);for(let u of i.bonds)n.get(u.a1.id)?.push(u),n.get(u.a2.id)?.push(u);for(let u of t){let m=n.get(u)??[];if(m.some(f=>f.kind===\"cross-polymer\"||f.kind===\"hbond\"))throw new j(\"gap-at-complex-junction\",`Gap atom ${u} participates in a cross-polymer/hbond bond`,{atomId:u});let h=m.filter(f=>f.kind===\"backbone\");if(h.length>2)throw new j(\"gap-at-complex-junction\",`Gap atom ${u} has ${h.length} backbone bonds (max 2 allowed)`,{atomId:u,bondCount:h.length})}let o=i.atoms.filter(u=>!t.has(u.id)),r=[],s=[];for(let u of i.chains){let m=u.backboneAtoms.filter(f=>!t.has(f.id)),p=(()=>{let f=0;for(let y of i.bonds)y.id>f&&(f=y.id);return f+1})(),h=[];for(let f of u.bonds)t.has(f.a1.id)||t.has(f.a2.id)||h.push(f);for(let f=0;f<u.backboneAtoms.length;f++){let y=u.backboneAtoms[f];if(!t.has(y.id))continue;let w=_r(u.backboneAtoms,f,t),_=vr(u.backboneAtoms,f,t);if(w===null||_===null)continue;let M={id:p++,a1:w,a2:_,kind:\"backbone\",r1:{kind:\"numeric\",r:2},r2:{kind:\"numeric\",r:1}};h.find(x=>x.a1.id===w.id&&x.a2.id===_.id)===void 0&&h.push(M);}for(let f of h)s.push(f);r.push({id:u.id,polymerType:u.polymerType,backboneAtoms:m,bonds:h,...u.annotation!==void 0?{annotation:u.annotation}:{}});}for(let u of i.bonds)u.kind!==\"cross-polymer\"&&u.kind!==\"hbond\"||t.has(u.a1.id)||t.has(u.a2.id)||s.push(u);let a=new Map;for(let u of r){let m=0;for(let p of u.backboneAtoms)m+=1,a.set(p.id,{...p,bio:{...p.bio,positionInChain:m}});}for(let u of o)a.has(u.id)||a.set(u.id,u);let l=r.map(u=>{let m=u.backboneAtoms.map(h=>a.get(h.id)),p=u.bonds.map(h=>({...h,a1:a.get(h.a1.id),a2:a.get(h.a2.id)}));return {id:u.id,polymerType:u.polymerType,backboneAtoms:m,bonds:p,...u.annotation!==void 0?{annotation:u.annotation}:{}}}),d=s.map(u=>({...u,a1:a.get(u.a1.id),a2:a.get(u.a2.id)}));return {mol:{atoms:o.map(u=>a.get(u.id)),bonds:d,chains:l,groups:i.groups,annotations:i.annotations},survivorByOldContinuousId:e}}function _r(i,e,t){for(let n=e-1;n>=0;n--){let o=i[n];if(o!==void 0&&!t.has(o.id))return o}return null}function vr(i,e,t){for(let n=e+1;n<i.length;n++){let o=i[n];if(o!==void 0&&!t.has(o.id))return o}return null}function yn(i,e,t){let n=t?.mode??\"lenient\",o=[];for(let s of wr)o.push(...s(i,e));let r=n===\"pedantic\"?o.map(s=>s.severity===\"warning\"?{...s,severity:\"error\"}:s):o;if(n===\"strict\"||n===\"pedantic\"){let s=r.filter(a=>a.severity===\"error\");if(s.length>0)throw new Ye(s)}return r}var wr=[xr,kr,Ar,Mr,Tr,Er,Cr,Lr];function xr(i,e){let t=[],n=new Set(i.chains.map(s=>s.id));for(let s of i.bonds)s.kind!==\"cross-polymer\"&&s.kind!==\"hbond\"||(n.has(s.a1.bio.chainId)||t.push({severity:\"error\",code:\"unknown-chain-reference\",message:`Connection references unknown chain '${s.a1.bio.chainId}'`,context:{chainId:s.a1.bio.chainId,bondId:s.id}}),n.has(s.a2.bio.chainId)||t.push({severity:\"error\",code:\"unknown-chain-reference\",message:`Connection references unknown chain '${s.a2.bio.chainId}'`,context:{chainId:s.a2.bio.chainId,bondId:s.id}}));for(let s of i.chains)for(let a of i.bonds){if(a.kind!==\"cross-polymer\"&&a.kind!==\"hbond\")continue;let l=0;for(let d of s.backboneAtoms)l+=d.branchAtom!==void 0?2:1;for(let d of [a.a1,a.a2]){if(d.bio.chainId!==s.id)continue;let c=le(d,s);(c<1||c>l)&&t.push({severity:\"error\",code:\"position-out-of-range\",message:`Position ${c} out of range for chain '${s.id}' (length ${l})`,context:{chainId:s.id,atomId:d.id,found:c}});}}let o=new Set;for(let s of i.groups)s.kind!==\"bracket\"&&o.add(s.id);for(let s of i.groups)if(s.kind!==\"bracket\")for(let a of s.members)n.has(a.target)||o.has(a.target)||t.push({severity:\"error\",code:\"unknown-group-reference\",message:`Group '${s.id}' references unknown id '${a.target}'`,context:{found:a.target}});let r=new Map;for(let s of i.groups){if(s.kind===\"bracket\")continue;let a=[];for(let l of s.members)o.has(l.target)&&a.push(l.target);r.set(s.id,a);}for(let s of r.keys()){let a=new Set,l=[s];for(;l.length>0;){let d=l.pop();if(a.has(d))continue;a.add(d);let c=r.get(d)??[];for(let u of c)u===s?t.push({severity:\"error\",code:\"group-cycle\",message:`Group cycle detected involving '${s}'`,context:{found:s}}):a.has(u)||l.push(u);}}return t}function kr(i,e){let t=[];if(e===null)return t;let n=new Map;for(let o of i.chains)n.set(o.id,o.polymerType);for(let o of i.atoms){let r=n.get(o.bio.chainId);if(r===void 0)continue;let s=o.monomer,a=s?.meta;if(s===null||a?.missing===true){t.push({severity:\"warning\",code:\"unresolved-monomer\",message:`Monomer '${o.symbol}' not found in library for ${r}`,context:{chainId:o.bio.chainId,atomId:o.id,found:o.symbol}});continue}a?.ambiguous!==true&&s.smiles!==void 0&&s.smiles.length>0&&(s.rgroups.length===0?t.push({severity:\"warning\",code:\"inline-smiles-without-r-groups\",message:`Inline-SMILES monomer '${s.symbol}' has no R-groups`,context:{atomId:o.id,found:s.symbol}}):s.rgroups.length>4&&t.push({severity:\"warning\",code:\"inline-smiles-too-many-rs\",message:`Inline-SMILES monomer '${s.symbol}' has ${s.rgroups.length} R-groups (max 4 expected)`,context:{atomId:o.id,found:s.rgroups.length}}));}for(let o of i.atoms){let r=n.get(o.bio.chainId);if(!(r===void 0||e.getMonomer(r,o.symbol)!==null)){for(let a of e.getMonomerSymbolsByType(r))if(a!==o.symbol&&a.toLowerCase()===o.symbol.toLowerCase()){t.push({severity:\"info\",code:\"case-mismatch\",message:`Symbol '${o.symbol}' differs from library entry '${a}' only in case`,context:{atomId:o.id,found:o.symbol,expected:a}});break}}}return t}function Ar(i,e){let t=[],n=new Map;for(let o of i.bonds)for(let[r,s]of [[o.a1,o.r1],[o.a2,o.r2]]){if(s.kind!==\"numeric\")continue;let a=n.get(r.id)??new Set;a.has(s.r)&&t.push({severity:\"error\",code:\"rgroup-already-bonded\",message:`R-group R${s.r} on atom ${r.id} already bonded`,context:{atomId:r.id,bondId:o.id,found:s.r}}),a.add(s.r),n.set(r.id,a);}for(let o of i.bonds){for(let[r,s]of [[o.a1,o.r1],[o.a2,o.r2]]){if(s.kind!==\"numeric\"||r.monomer===null)continue;let a=r.monomer.rs;(s.r<1||s.r>a)&&t.push({severity:\"error\",code:\"rgroup-not-on-monomer\",message:`R-group R${s.r} not defined on monomer '${r.symbol}' (rs=${a})`,context:{atomId:r.id,bondId:o.id,found:s.r,expected:`R1..R${a}`}});}o.kind===\"backbone\"&&o.r1.kind===\"numeric\"&&o.r2.kind===\"numeric\"&&(o.r1.r===2&&o.r2.r===1||t.push({severity:\"warning\",code:\"backbone-rgroup-misaligned\",message:`Backbone bond uses R${o.r1.r}->R${o.r2.r} (expected R2->R1)`,context:{bondId:o.id,found:`R${o.r1.r}->R${o.r2.r}`}})),o.kind===\"branch\"&&o.r1.kind===\"numeric\"&&o.r1.r!==3&&t.push({severity:\"warning\",code:\"branch-rgroup-misaligned\",message:`Branch bond uses R${o.r1.r} (expected R3 on parent)`,context:{bondId:o.id,found:`R${o.r1.r}`}});}for(let o of i.atoms){if(o.monomer===null)continue;let s=n.get(o.id)?.size??0;if(o.monomer.rs>s){let a=o.monomer.rs-s;a>0&&o.monomer.rs>0&&t.push({severity:\"info\",code:\"unmatched-r-group\",message:`Monomer '${o.symbol}' on atom ${o.id} has ${a} unused R-group(s); default cap applied`,context:{atomId:o.id,found:a}});}}return t}function Mr(i,e){let t=[];for(let n of i.chains){if(n.polymerType===\"CHEM\"&&n.backboneAtoms.length>1&&t.push({severity:\"error\",code:\"chem-multiple-monomers\",message:`CHEM polymer '${n.id}' has ${n.backboneAtoms.length} monomers (expected 1)`,context:{chainId:n.id,found:n.backboneAtoms.length}}),n.polymerType===\"BLOB\")for(let o of n.backboneAtoms)o.bio.blobtype===void 0&&o.symbol!==\"Bead\"&&o.symbol!==\"Group\"&&t.push({severity:\"error\",code:\"blob-non-blob-symbol\",message:`BLOB '${n.id}' contains non-blob symbol '${o.symbol}'`,context:{chainId:n.id,atomId:o.id,found:o.symbol}});if(n.polymerType===\"RNA\"){let o=false;for(let r=0;r<n.backboneAtoms.length;r++){let s=n.backboneAtoms[r];s.biotype===b.BASE&&!o&&t.push({severity:\"error\",code:\"rna-bare-base\",message:`Bare base '${s.symbol}' without parent sugar in '${n.id}'`,context:{chainId:n.id,atomId:s.id}}),s.biotype===b.LINKER&&(n.backboneAtoms.slice(0,r).some(l=>l.biotype===b.SUGAR)||t.push({severity:\"warning\",code:\"rna-bare-linker\",message:`Bare linker '${s.symbol}' before any sugar in '${n.id}'`,context:{chainId:n.id,atomId:s.id}})),o=s.biotype===b.SUGAR||s.biotype===b.LINKER;}}}return t}function Tr(i,e){let t=[],n=new Map;for(let r of i.chains)n.set(r.id,r.polymerType);let o=new Map;for(let r of i.bonds){if(r.kind!==\"hbond\")continue;o.set(r.a1.id,(o.get(r.a1.id)??0)+1),o.set(r.a2.id,(o.get(r.a2.id)??0)+1);let s=n.get(r.a1.bio.chainId),a=n.get(r.a2.bio.chainId);(s!==\"RNA\"||a!==\"RNA\")&&t.push({severity:\"error\",code:\"pair-non-rna\",message:`Hydrogen-bond connects non-RNA chains (${s}/${a})`,context:{bondId:r.id}}),(r.a1.biotype!==b.BASE||r.a2.biotype!==b.BASE)&&t.push({severity:\"warning\",code:\"pair-position-not-base\",message:\"Hydrogen-bond endpoints are not both bases\",context:{bondId:r.id,found:`${r.a1.biotype}/${r.a2.biotype}`}}),Sr(r.a1.symbol,r.a2.symbol)||t.push({severity:\"warning\",code:\"pair-non-canonical\",message:`Non-canonical pair ${r.a1.symbol}-${r.a2.symbol}`,context:{bondId:r.id,found:`${r.a1.symbol}-${r.a2.symbol}`}});}for(let[r,s]of o)s>1&&t.push({severity:\"warning\",code:\"pair-already-paired\",message:`Base atom ${r} participates in ${s} pair bonds`,context:{atomId:r,found:s}});return t}function Sr(i,e){let t=i.toUpperCase(),n=e.toUpperCase();return new Set([\"A:T\",\"T:A\",\"A:U\",\"U:A\",\"G:C\",\"C:G\"]).has(`${t}:${n}`)}function Er(i,e){let t=[];for(let n of i.atoms){let o=n.bio.ambiguity;if(o!==void 0){if(n.bio.ambiguityKind===\"and\"){let r=yo(o,\"+\");for(let s of r)s.ratio!==void 0&&s.ratio<0&&t.push({severity:\"error\",code:\"ratio-and-negative\",message:`AND ratio for '${s.symbol}' is negative (${s.ratio})`,context:{atomId:n.id,found:s.ratio}});}else if(n.bio.ambiguityKind===\"or\"){let r=yo(o,\",\"),s=0,a=false;for(let l of r)typeof l.ratio==\"number\"&&(s+=l.ratio,a=true);a&&Math.abs(s-1)>.001&&Math.abs(s-100)>.5&&t.push({severity:\"info\",code:\"ratio-doesnt-sum-to-1\",message:`OR ratios sum to ${s} (expected 1.0 or 100)`,context:{atomId:n.id,found:s}});}}}return t}function yo(i,e){let t=i.trim();t.startsWith(\"(\")&&t.endsWith(\")\")&&(t=t.slice(1,-1));let n=t.split(e),o=[];for(let r of n){let s=r.trim();if(s.length===0)continue;let a=s.indexOf(\":\");if(a<0){o.push({symbol:s});continue}let l=s.slice(0,a),d=s.slice(a+1),c=parseFloat(d);Number.isFinite(c)?o.push({symbol:l,ratio:c}):o.push({symbol:l});}return o}function Cr(i,e){let t=[],n=new Set(i.chains.map(o=>o.id));for(let o of i.annotations.perPolymer.keys())n.has(o)||t.push({severity:\"warning\",code:\"annotation-unknown-polymer\",message:`Annotation references unknown polymer '${o}'`,context:{found:o}});return t}function Lr(i,e){let t=[];for(let o of i.chains)o.backboneAtoms.length>1e4&&t.push({severity:\"info\",code:\"polymer-too-long\",message:`Polymer '${o.id}' has ${o.backboneAtoms.length} atoms (> 10000); renderer may switch to rows layout`,context:{chainId:o.id,found:o.backboneAtoms.length}});let n=0;for(let o of i.bonds)(o.kind===\"cross-polymer\"||o.kind===\"hbond\")&&(n+=1);n>1e3&&t.push({severity:\"info\",code:\"connection-count-high\",message:`${n} cross-polymer/hbond connections (> 1000); rendering may be slow`,context:{found:n}});for(let o of i.groups)o.kind===\"bracket\"&&o.repeat!==void 0&&o.repeat.max>1e4&&t.push({severity:\"warning\",code:\"bracket-repeat-too-large\",message:`Bracket repeat upper bound ${o.repeat.max} > 10000`,context:{found:o.repeat.max}});return t}function go(i){let e=[],t=new Map;for(let n of i.chains)for(let o of n.backboneAtoms)t.set(o.id,n.id);for(let n of i.chains)for(let o of n.backboneAtoms)o.branchAtom!==void 0&&t.set(o.branchAtom.id,n.id);for(let n of i.chains){let o=Br(n.polymerType),r=n.backboneAtoms,s=[],a=[],l=[];for(let c of n.bonds)c.kind===\"backbone\"&&l.push(c);if(o===\"RNA\")for(let c of r){if(c.biotype!==b.SUGAR){s.push(null),a.push(null);continue}let u=null,m=null;for(let p of n.bonds){if(p.kind!==\"branch\")continue;let h=p.a1.id===c.id?p.a2:p.a2.id===c.id?p.a1:null;if(h!==null&&h.biotype===b.BASE){u=h,m=p;break}}s.push(u),a.push(m);}else for(let c=0;c<r.length;c++)s.push(null),a.push(null);let d=Rr(i,n.id,r,t);e.push({id:n.id,polymerType:o,backbone:r,bases:s,backboneBonds:l,baseBonds:a,isCyclic:d,...n.strandType!==void 0?{strandType:n.strandType}:{}});}return e}function Br(i){switch(i){case v.PEPTIDE:return \"PEPTIDE\";case v.RNA:return \"RNA\";case v.CHEM:return \"CHEM\";case v.BLOB:return \"BLOB\";default:return \"BLOB\"}}function Rr(i,e,t,n){if(t.length<2)return  false;let o=t[0],r=t[t.length-1];for(let s of i.bonds){if(s.kind===\"backbone\"||s.kind===\"branch\")continue;let a=n.get(s.a1.id),l=n.get(s.a2.id);if(a!==e||l!==e||!(s.a1.id===r.id&&s.a2.id===o.id||s.a2.id===r.id&&s.a1.id===o.id))continue;let c=s.a1.id===o.id?s.r1:s.r2,u=s.a1.id===r.id?s.r1:s.r2,m=c.kind===\"numeric\"&&c.r===1,p=u.kind===\"numeric\"&&u.r===2;if(m&&p)return  true}return  false}var gn=44.800000000000004,_o=1.5*28,At=1.5*28/gn,_n=1.5*28/gn,vn=1.5*28/gn;function ke(i,e){let t=e?.bondLength??28,n=e?.origin??{x:0,y:0},o=1.6*t,r=new Map;for(let s=0;s<i.backbone.length;s++){let a=i.backbone[s];r.set(a.id,{x:n.x+s*o,y:n.y});}return r}var Ir=Math.PI/180;function Mt(i,e){let t=i.backbone.length;if(t<=2){let d={};return e?.bondLength!==void 0&&(d.bondLength=e.bondLength),e?.origin!==void 0&&(d.origin=e.origin),ke(i,d)}let n=e?.bondLength??28,o=e?.origin??{x:0,y:0},r=e?.startDegrees??-90,a=1.6*n/(2*Math.sin(Math.PI/t)),l=new Map;for(let d=0;d<t;d++){let c=i.backbone[d],m=(r+d*360/t)*Ir;l.set(c.id,{x:o.x+a*Math.cos(m),y:o.y+a*Math.sin(m)});}return l}var Pr=10,Hr=1.5/1.6;function vo(i,e){let t=e?.bondLength??28,n=e?.origin??{x:0,y:0},o=Math.max(1,e?.perRow??Pr),r=e?.rowSpacing??Hr,s=1.6*t,a=r*s,l=new Map;for(let d=0;d<i.backbone.length;d++){let c=i.backbone[d],u=Math.floor(d/o),m=d%o,p=u%2===0?n.x+m*s:n.x+(o-1-m)*s,h=n.y+u*a;l.set(c.id,{x:p,y:h});}return l}function wo(i,e){let t=new Map;for(let r=0;r<i.backbone.length;r++)t.set(i.backbone[r].id,r);let n=i.backbone.length-1,o=[];for(let r of e.bonds){if(r.kind===\"backbone\"||r.kind===\"branch\")continue;let s=t.get(r.a1.id),a=t.get(r.a2.id);if(s===void 0||a===void 0)continue;let l=Math.min(s,a),d=Math.max(s,a);d-l<2||l===0&&d===n||o.push({lo:l,hi:d});}return o}function xo(i,e){return e===null?false:wo(i,e).length>0}function wn(i,e,t){if(e===null)return ke(i,t);let n=t?.bondLength??28,o=t?.origin??{x:0,y:0},r=1.6*n,s=wo(i,e);if(s.length===0)return ke(i,t);let a=s[0].lo,l=s[0].hi;for(let L of s)L.lo<a&&(a=L.lo),L.hi>l&&(l=L.hi);let d=i.backbone.slice(a,l+1),c=d.length,u=r/(2*Math.sin(Math.PI/c)),m={id:i.id,polymerType:i.polymerType,backbone:d,bases:new Array(c).fill(null),baseBonds:new Array(c).fill(null)},p=a,h={x:o.x+p*r+u,y:o.y},f=Mt(m,{bondLength:n,origin:h,startDegrees:180}),y=new Map;for(let L=0;L<a;L++){let z=i.backbone[L];y.set(z.id,{x:o.x+L*r,y:o.y});}for(let[L,z]of f)y.set(L,z);let w=d[c-1],_=f.get(w.id)??h,M=_.x-h.x,k=_.y-h.y,x=Math.hypot(M,k);x<1e-6&&(M=0,k=1,x=1);let T=M/x,E=k/x,C={x:_.x+T*r,y:_.y+E*r},P=Math.sign(_.x-h.x);if(P===0&&c>=2){let L=f.get(d[c-2].id);L!==void 0&&(P=Math.sign(_.x-L.x));}P===0&&(P=1);for(let L=l+1;L<i.backbone.length;L++){let z=i.backbone[L],ae=L-(l+1);y.set(z.id,ae===0?C:{x:C.x+P*r*ae,y:C.y});}return y}function Ao(i){let e=new Map,t=new Map;for(let n=0;n<i.backbone.length;n++){e.set(i.backbone[n].id,n);let o=i.bases[n];o!=null&&t.set(o.id,n);}return {sugarToIdx:e,baseToIdx:t}}function ko(i,e,t){let n=e.get(i);if(n!==void 0)return n;let o=t.get(i);return o!==void 0?o:null}function Mo(i,e,t){let n=i.kind===\"hbond\",o=i.kind===\"cross-polymer\"&&typeof i.r1==\"object\"&&i.r1!==null&&i.r1.kind===\"pair\"&&typeof i.r2==\"object\"&&i.r2!==null&&i.r2.kind===\"pair\";if(!n&&!o)return null;let r=ko(i.a1.id,e,t),s=ko(i.a2.id,e,t);return r===null||s===null||r===s?null:{lo:Math.min(r,s),hi:Math.max(r,s)}}function To(i,e){if(i.polymerType!==\"RNA\"||i.backbone.length===0)return  false;let{sugarToIdx:t,baseToIdx:n}=Ao(i);for(let o of e.bonds)if(Mo(o,t,n)!==null)return  true;return  false}function $r(i,e){let t=i.backbone.length,n=new Int32Array(t).fill(-1);if(t===0)return n;let{sugarToIdx:o,baseToIdx:r}=Ao(i),s=[];for(let l of e.bonds){let d=Mo(l,o,r);d!==null&&s.push([d.lo,d.hi]);}s.sort((l,d)=>l[0]-d[0]||d[1]-l[1]);let a=[];for(let l of s){let[d,c]=l,u=false;for(let[m,p]of a){let h=c<m||d>p,f=d>m&&c<p||d<m&&c>p;if(!h&&!f){u=true;break}}u||n[d]!==-1||n[c]!==-1||(n[d]=c,n[c]=d,a.push(l));}return n}function Dr(i){return e(0,i.length-1,null);function e(t,n,o){let r=[],s=-1,a=t;for(;a<=n;){let l=i[a];if(l>a&&l<=n){s!==-1&&(r.push({kind:\"unpaired\",from:s,to:a-1}),s=-1);let d=1;for(;a+2*d<l-2*d&&i[a+2*d]===l-2*d&&i[a+2*d-1]===-1&&i[l-2*d+1]===-1;)d+=1;let c=a+2*(d-1),u=l-2*(d-1),m=[c,u],p=e(c+1,u-1,m);r.push({kind:\"stem\",fromIdx:a,toIdx:l,numPairs:d,child:p}),a=l+1;}else s===-1&&(s=a),a+=1;}return s!==-1&&r.push({kind:\"unpaired\",from:s,to:n}),{kind:\"loop\",nodes:r,closingPair:o}}}function Tt(i){let e=Math.hypot(i.x,i.y);return e===0?{x:1,y:0}:{x:i.x/e,y:i.y/e}}function Or(i){return {x:-i.y,y:i.x}}function xn(i,e,t){return {x:i.x+e*Math.cos(t),y:i.y+e*Math.sin(t)}}function Nr(i,e,t,n){let o=t+n+1;if(o<=0)return Math.max(i/2+1,e);let r=n+1,s=o*e,a=Math.max(s/(2*Math.PI),i/2+1);for(let l=0;l<64;l++){let d=i/(2*a),u=2*Math.asin(Math.min(.9999,Math.max(-0.9999,d))),m=(2*Math.PI-r*u)*a-s,p=d,h=Math.sqrt(Math.max(1e-12,1-p*p)),y=2*(-i/(2*a*a)/h),w=2*Math.PI-r*u-r*a*y;if(!Number.isFinite(w)||Math.abs(w)<1e-12)break;let _=m/w,M=a-_;if(!Number.isFinite(M)||M<i/2+.001){a=i/2+.001;break}if(a=M,Math.abs(_)<1e-9)break}return Math.max(a,i/2+.001)}function St(i,e,t,n,o){let r=o.chain.bases[i];r!=null&&o.out.set(r.id,{x:e.x+n*t.x,y:e.y+n*t.y});}function So(i,e,t){let{chain:n,step:o,rail:r,baseInwardHang:s,out:a}=t,l=2*i.numPairs-1,d={x:e.normal.x,y:e.normal.y},c={x:-e.normal.x,y:-e.normal.y};for(let m=0;m<l;m++){let p=n.backbone[i.fromIdx+m],h=n.backbone[i.toIdx-m],f=m*o,y={x:e.origin.x+f*e.tangent.x,y:e.origin.y+f*e.tangent.y},w={x:e.origin.x+f*e.tangent.x+r*e.normal.x,y:e.origin.y+f*e.tangent.y+r*e.normal.y};a.set(p.id,y),a.set(h.id,w),St(i.fromIdx+m,y,d,s,t),St(i.toIdx-m,w,c,s,t);}let u=(l-1)*o;return {origin:{x:e.origin.x+u*e.tangent.x,y:e.origin.y+u*e.tangent.y},tangent:e.tangent,normal:e.normal}}function Eo(i,e,t,n){if(i.closingPair===null)return;let{step:o,rail:r,out:s}=t,a=0,l=0;for(let T of i.nodes)T.kind===\"unpaired\"?a+=T.to-T.from+1:l+=1;let d=Nr(r,o,a,l),c=s.get(t.chain.backbone[i.closingPair[0]].id),u=s.get(t.chain.backbone[i.closingPair[1]].id),m={x:(c.x+u.x)/2,y:(c.y+u.y)/2},p=Math.sqrt(Math.max(0,d*d-r/2*(r/2))),h={x:m.x+p*e.tangent.x,y:m.y+p*e.tangent.y},f=Math.atan2(c.y-h.y,c.x-h.x),w=Math.atan2(u.y-h.y,u.x-h.x)-f;for(;w>Math.PI;)w-=2*Math.PI;for(;w<=-Math.PI;)w+=2*Math.PI;let _=w>0?-1:1,M=2*Math.asin(Math.min(.9999,Math.max(-0.9999,r/(2*d)))),k=o/d,x=f;for(let T of i.nodes)if(T.kind===\"unpaired\")for(let E=T.from;E<=T.to;E++){x=x+_*k;let C=xn(h,d,x);s.set(t.chain.backbone[E].id,C);let P=Tt({x:C.x-h.x,y:C.y-h.y});St(E,C,P,t.step,t);}else {x=x+_*k;let E=xn(h,d,x);x=x+_*M;let C=xn(h,d,x);s.set(t.chain.backbone[T.fromIdx].id,E),s.set(t.chain.backbone[T.toIdx].id,C);let P=Tt({x:(E.x+C.x)/2-h.x,y:(E.y+C.y)/2-h.y}),L=Tt({x:C.x-E.x,y:C.y-E.y}),ae=So(T,{origin:E,tangent:P,normal:L},t);Eo(T.child,ae,t);}}function Fr(i,e,t){let{step:n,rail:o,out:r}=t,s={x:e.origin.x,y:e.origin.y},a={x:e.tangent.x,y:e.tangent.y},l={x:-e.normal.x,y:-e.normal.y};for(let d of i.nodes)if(d.kind===\"unpaired\")for(let c=d.from;c<=d.to;c++){let u={x:s.x,y:s.y};r.set(t.chain.backbone[c].id,u),St(c,u,{x:e.normal.x,y:e.normal.y},t.step,t),s={x:s.x+n*a.x,y:s.y+n*a.y};}else {let c={origin:{x:s.x,y:s.y},tangent:l,normal:a},u=So(d,c,t);Eo(d.child,u,t),s={x:s.x+(o+n)*a.x,y:s.y+(o+n)*a.y};}}function Co(i,e,t){let n=t?.bondLength??28,o=1.6*n,r=o/2,a=_o*(n/28)+2*r,l=t?.origin??{x:0,y:0},d=Tt(t?.rootDirection??{x:1,y:0}),c=Or(d),u=new Map;if(i.backbone.length===0)return u;let m=$r(i,e),p=Dr(m);Fr(p,{origin:l,tangent:d,normal:c},{chain:i,step:o,rail:a,baseInwardHang:r,out:u});for(let y of i.backbone)u.has(y.id)||u.set(y.id,{x:l.x,y:l.y});return u}function Lo(i,e,t){if(i.polymerType!==\"RNA\")return e;let n=t?.bondLength??28,o=1.6*n;for(let r=0;r<i.backbone.length;r++){let s=i.bases[r];if(s==null||e.has(s.id))continue;let a=i.backbone[r],l=e.get(a.id);if(l===void 0)continue;let d=Gr(i,r,e);e.set(s.id,{x:l.x+o*d.x,y:l.y+o*d.y});}return e}function Gr(i,e,t){let n=i.backbone[e],o=t.get(n.id);if(o===void 0)return {x:0,y:1};let r=e>0?i.backbone[e-1]:void 0,s=e<i.backbone.length-1?i.backbone[e+1]:void 0,a=r!==void 0?t.get(r.id):void 0,l=s!==void 0?t.get(s.id):void 0,d=0,c=0;if(a!==void 0&&l!==void 0){let u=l.x-a.x,m=l.y-a.y,p=Math.hypot(u,m);if(p===0)return {x:0,y:1};let h={x:m/p,y:-u/p},f={x:-m/p,y:u/p},y=h.y>=f.y?h:f;d=y.x,c=y.y;}else if(l!==void 0){let u=l.x-o.x,m=l.y-o.y,p=Math.hypot(u,m);if(p===0)return {x:0,y:1};let h={x:m/p,y:-u/p},f={x:-m/p,y:u/p},y=h.y>=f.y?h:f;d=y.x,c=y.y;}else if(a!==void 0){let u=o.x-a.x,m=o.y-a.y,p=Math.hypot(u,m);if(p===0)return {x:0,y:1};let h={x:m/p,y:-u/p},f={x:-m/p,y:u/p},y=h.y>=f.y?h:f;d=y.x,c=y.y;}else return {x:0,y:1};return {x:d,y:c}}function Io(i,e,t,n){let o=n?.bondLength??28,r=1.6*o,s=new Map,a=new Map;for(let h of i){let f=new Set;for(let y of h.backbone)f.add(y.id);for(let y of h.bases)y!==null&&f.add(y.id);a.set(h.id,{chain:h,atomIds:f});for(let y of f)s.set(y,h);}let l=new Set;if(i.length>0){let h=i.find(f=>f.strandType===\"ss\");l.add((h??i[0]).id);}let d=new Map;for(let h of i)d.set(h.id,h.id);let c=h=>{let f=h;for(;d.get(f)!==f;)f=d.get(f);let y=h;for(;d.get(y)!==f;){let w=d.get(y);d.set(y,f),y=w;}return f},u=(h,f)=>{d.set(c(h),c(f));},m=h=>{let f=c(h),y=new Set;for(let[w,_]of a)if(c(w)===f)for(let M of _.atomIds)y.add(M);return y},p=h=>{let f=c(h),y=0;for(let w of d.keys())c(w)===f&&(y+=1);return y};for(let h of t.bonds){if(h.kind===\"backbone\"||h.kind===\"branch\")continue;let f=s.get(h.a1.id),y=s.get(h.a2.id);if(f===void 0||y===void 0||f.id===y.id)continue;h.kind===\"hbond\"&&(f.strandType===\"as\"&&y.strandType===\"ss\"?l.add(y.id):y.strandType===\"as\"&&f.strandType===\"ss\"?l.add(f.id):f.strandType===\"as\"&&!l.has(y.id)?l.add(y.id):y.strandType===\"as\"&&!l.has(f.id)&&l.add(f.id));let w=y,_=h.a1,M=h.a2;if(l.has(y.id)&&!l.has(f.id))w=f,_=h.a2,M=h.a1;else if(!l.has(f.id)&&!l.has(y.id)){if(l.size>0){let T=new Set;for(let L of l){let z=a.get(L);if(z!==void 0)for(let ae of z.atomIds)T.add(ae);}let E=Ho(T,e),C=a.get(f.id),P=Po(C.atomIds,e);if(E!==null&&P!==null){let L=E+r*At-P;L>0&&tt(C.atomIds,e,0,L);}}l.add(f.id),w=y,_=h.a1,M=h.a2;}else if(l.has(f.id)&&l.has(y.id)){if(c(f.id)===c(y.id)||h.kind!==\"cross-polymer\")continue;let T=m(f.id),E=m(y.id),C=T.size<=E.size,P=C?T:E,L=C?E:T,z=e.get((C?h.a1:h.a2).id),ae=e.get((C?h.a2:h.a1).id);z!==void 0&&ae!==void 0&&Ro(P,z,L,ae,r,e),u(f.id,y.id);continue}let k=e.get(_.id),x=e.get(M.id);if(!(k===void 0||x===void 0)){if(h.kind===\"hbond\"){let T=a.get(w.id);Vr(T.atomIds,e),Ur(T.atomIds,e);let E=e.get(M.id),C=k.x-E.x,P=k.y+r*_n-E.y;P=Bo(P,T,l,a,e,r*_n),tt(T.atomIds,e,C,P);}else if(w.isCyclic&&w.backbone.length>=3){let T=a.get(w.id),E=w.id===f.id?y:f,C=a.get(E.id);Kr(T.atomIds,x,C.atomIds,k,r,e);}else {let T=a.get(w.id),E=k.x-x.x,C=k.y+r*vn-x.y;C=Bo(C,T,l,a,e,r*vn);let P=Math.abs(x.y+C-k.y),L=s.get(_.id),z=L!==void 0&&p(L.id)>1;h.kind===\"cross-polymer\"&&z&&P>2*r?Ro(T.atomIds,x,m(L.id),k,r,e):tt(T.atomIds,e,E,C);}l.add(w.id),u(f.id,y.id);}}return l}function Bo(i,e,t,n,o,r){let s=Po(e.atomIds,o);if(s===null)return i;let a=null;for(let c of t){let u=n.get(c);if(u===void 0)continue;let m=Ho(u.atomIds,o);m!==null&&(a===null||m>a)&&(a=m);}if(a===null)return i;let l=s+i,d=a+r;return l<d?d-s:i}function Po(i,e){let t=null;for(let n of i){let o=e.get(n);o!==void 0&&(t===null||o.y<t)&&(t=o.y);}return t}function Ho(i,e){let t=null;for(let n of i){let o=e.get(n);o!==void 0&&(t===null||o.y>t)&&(t=o.y);}return t}function tt(i,e,t,n){for(let o of i){let r=e.get(o);r!==void 0&&e.set(o,{x:r.x+t,y:r.y+n});}}function Vr(i,e){let t=0,n=0;for(let r of i){let s=e.get(r);s!==void 0&&(t+=s.x,n+=1);}if(n===0)return;let o=t/n;for(let r of i){let s=e.get(r);s!==void 0&&e.set(r,{x:2*o-s.x,y:s.y});}}function 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0&&i.tag!==\"\"&&m.push(R(\"circle\",{class:\"hw-atom__tag-dot\",cx:i.p.x+r.size*.7,cy:i.p.y-r.size*.7,r:Math.max(2,t*.18),fill:e.tagDotColor}));let h=fs(i);return R(\"g\",{class:\"hw-atom\",\"data-atom-id\":i.id,\"data-symbol\":i.symbol,\"data-chain-id\":i.bio.chainId,\"data-biotype\":i.biotype,\"data-testid\":`canvas-atom-${i.id}`,tabindex:0,role:\"button\",\"aria-label\":h},m.join(\"\"))}function fs(i){let e=i.symbol===\"\"?\"?\":i.symbol,t=i.bio.chainId===\"\"?\"unknown chain\":i.bio.chainId,n=i.bio.positionInChain;return `${e} at position ${n} of ${t}`}function bs(i,e,t){let n=[];for(let o of i.bonds){if(o.ratio===void 0)continue;let r=(o.a1.p.x+o.a2.p.x)/2,s=(o.a1.p.y+o.a2.p.y)/2,a=o.ratio.denominator!==void 0?`${o.ratio.numerator}/${o.ratio.denominator}`:`${o.ratio.numerator}`;n.push(R(\"text\",{class:\"hw-annotation hw-annotation--bond-ratio\",x:r,y:s-t*.4,\"text-anchor\":\"middle\",\"font-size\":t*.7,\"font-family\":e.fontFamily,fill:e.annotationColor},de(a)));}for(let o of i.atoms){let r=o.bio.annotation;if(r===void 0||r===\"\")continue;let s=he(o,e);n.push(R(\"text\",{class:\"hw-annotation hw-annotation--atom\",x:o.p.x+s.size+2,y:o.p.y-s.size,\"font-size\":t*.7,\"font-family\":e.fontFamily,fill:e.annotationColor},de(r)));}for(let o of i.chains){if(o.annotation===void 0||o.annotation===\"\")continue;let r=o.backboneAtoms[0];r!==void 0&&n.push(R(\"text\",{class:\"hw-annotation hw-annotation--chain\",x:r.p.x,y:r.p.y-e.fontSize*1.4,\"font-size\":t*.8,\"font-family\":e.fontFamily,fill:e.annotationColor},de(o.annotation)));}for(let o of i.chains){if(o.polymerType!==\"RNA\")continue;let r=o.backboneAtoms;if(r.length<2)continue;let s=r[0],a=r[r.length-1],l=r.length>=2?r[1]:null,d=r.length>=2?r[r.length-2]:null,c=e.fontSize*1.4,u=Xo(s.p,l?.p??null,c),m=Xo(a.p,d?.p??null,c),p=o.strandType!==void 0?`5'${o.strandType}`:\"5'\",h=o.strandType!==void 0?`3'${o.strandType}`:\"3'\";n.push(R(\"text\",{class:\"hw-annotation hw-annotation--prime 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0&&(i.fillStyle=n.backColor,i.fillRect(t.x,t.y,t.width,t.height)),i.translate(l,d),i.scale(a.scale,a.scale),i.translate(-s.x,-s.y),vs(i,e,o),xs(i,e,o,n.fontSize??o.fontSize,n.showIds??false,n.bondLength??o.bondLength),n.showAnnotations!==false&&ws(i,e,o,n.fontSize??o.fontSize),i.restore(),{bbox:{x:s.x,y:s.y,width:s.width,height:s.height},drawBox:{x:l,y:d,width:a.width,height:a.height}}}async function ei(i,e={}){let t=ys();if(t===null&&e.canvas===void 0)throw new Error(\"renderToPng: OffscreenCanvas is not available in this environment\");let n=e.theme??H,o=e.width??400,r=e.height??100,s=e.pixelRatio??1,a=e.canvas??new t(Math.max(1,Math.round(o*s)),Math.max(1,Math.round(r*s))),l=a.getContext(\"2d\");if(l===null)throw new Error(\"renderToPng: failed to acquire 2D context\");l.save(),l.scale(s,s),It(l,i,{x:0,y:0,width:o,height:r},{...e,backColor:e.backColor??n.background}),l.restore();let d=a;if(typeof d.convertToBlob!=\"function\")throw new Error(\"renderToPng: canvas.convertToBlob is not available\");let u=await(await d.convertToBlob({type:\"image/png\"})).arrayBuffer();return new Uint8Array(u)}function ys(){let i=globalThis;return typeof i.OffscreenCanvas==\"function\"?i.OffscreenCanvas:null}function gs(i,e){if(i.atoms.length===0)return {x:0,y:0,width:0,height:0};let t=pe(i.atoms[0],e);for(let n=1;n<i.atoms.length;n++)t=Et(t,pe(i.atoms[n],e));return t}function _s(i,e,t,n,o=1){let r=Math.max(0,e-2*n),s=Math.max(0,t-2*n),a=1;if(i.width>0||i.height>0){let c=i.width>0?r/i.width:Number.POSITIVE_INFINITY,u=i.height>0?s/i.height:Number.POSITIVE_INFINITY;a=Math.min(c,u,o),(!Number.isFinite(a)||a<=0)&&(a=1);}let l=i.width*a,d=i.height*a;return {x:(e-l)/2,y:(t-d)/2,width:l,height:d,scale:a}}function vs(i,e,t){for(let n of e.bonds)i.save(),i.strokeStyle=As(n,t),i.lineWidth=Ms(),n.kind===\"hbond\"?i.setLineDash([4,3]):i.setLineDash([]),i.beginPath(),i.moveTo(n.a1.p.x,n.a1.p.y),i.lineTo(n.a2.p.x,n.a2.p.y),i.stroke(),i.restore();}function ws(i,e,t,n){i.save(),i.fillStyle=t.annotationColor,i.font=`${n*.7}px ${t.fontFamily}`,i.textAlign=\"left\",i.textBaseline=\"alphabetic\";for(let r of e.atoms){let s=r.bio.annotation;if(s===void 0||s===\"\")continue;let a=he(r,t);i.fillText(s,r.p.x+a.size+2,r.p.y-a.size);}i.font=`${n*.8}px ${t.fontFamily}`;for(let r of e.chains){if(r.annotation===void 0||r.annotation===\"\")continue;let s=r.backboneAtoms[0];s!==void 0&&i.fillText(r.annotation,s.p.x,s.p.y-t.fontSize*1.4);}i.font=`bold ${n*.85}px ${t.fontFamily}`,i.textAlign=\"center\",i.textBaseline=\"middle\";let o=t.fontSize*1.4;for(let r of e.chains){if(r.polymerType!==\"RNA\")continue;let s=r.backboneAtoms;if(s.length<2)continue;let a=s[0],l=s[s.length-1],d=s.length>=2?s[1]:null,c=s.length>=2?s[s.length-2]:null,u=Jo(a.p,d?.p??null,o),m=Jo(l.p,c?.p??null,o),p=r.strandType!==void 0?`5'${r.strandType}`:\"5'\",h=r.strandType!==void 0?`3'${r.strandType}`:\"3'\";i.fillText(p,u.x,u.y),i.fillText(h,m.x,m.y);}i.restore();}function Jo(i,e,t){if(e===null)return {x:i.x-t,y:i.y};let n=i.x-e.x,o=i.y-e.y,r=Math.hypot(n,o);return r===0?{x:i.x-t,y:i.y}:{x:i.x+t*(n/r),y:i.y+t*(o/r)}}function xs(i,e,t,n,o=false,r=t.bondLength){for(let s of e.atoms){if(s.hidden)continue;let a=he(s,t),l=$(s.monomer,s.biotype,t.colorTheme);i.save(),i.fillStyle=l.background,i.strokeStyle=l.background,i.lineWidth=a.strokeWidth,i.lineJoin=\"round\",i.lineCap=\"round\",s.symbol===\"*\"?i.setLineDash([3,3]):i.setLineDash([]),ks(i,s,a.size,a.cornerRadius??0),i.fill(),i.stroke(),i.restore();let d=s.monomer?.symbol??s.symbol;if(d!==\"\"){let c=d.length<=1?1:Math.min(1,2/d.length),u=n*c;i.save(),i.fillStyle=l.text,i.font=`${u}px ${t.fontFamily}`,i.textAlign=\"center\",i.textBaseline=\"middle\",i.fillText(d,s.p.x,s.p.y),i.restore();}if(o){let c=r*Cn;i.save(),i.fillStyle=t.idColor,i.font=`${n*Ln}px ${t.fontFamily}`,i.textAlign=\"right\",i.textBaseline=\"bottom\",i.fillText(String(s.bio.continuousId),s.p.x-c,s.p.y-c),i.restore();}}}function ks(i,e,t,n){let o=e.p,r=e.symbol===\"*\"?\"circle\":Lt(e.biotype);switch(i.beginPath(),r){case \"hexagon\":Zo(i,o,6,t,-30);break;case \"diamond\":i.moveTo(o.x,o.y-t),i.lineTo(o.x+t,o.y),i.lineTo(o.x,o.y+t),i.lineTo(o.x-t,o.y),i.closePath();break;case \"pentagon\":Zo(i,o,5,t,-90);break;case \"rounded-rect\":case \"blob\":{let s=t/2,a=Math.max(0,Math.min(n,s)),l=o.x-s,d=o.y-s,c=s*2,u=s*2;i.moveTo(l+a,d),i.lineTo(l+c-a,d),i.quadraticCurveTo(l+c,d,l+c,d+a),i.lineTo(l+c,d+u-a),i.quadraticCurveTo(l+c,d+u,l+c-a,d+u),i.lineTo(l+a,d+u),i.quadraticCurveTo(l,d+u,l,d+u-a),i.lineTo(l,d+a),i.quadraticCurveTo(l,d,l+a,d),i.closePath();break}case \"circle\":i.ellipse(o.x,o.y,t,t,0,0,Math.PI*2);break}}function Zo(i,e,t,n,o){let r=360/t;for(let s=0;s<t;s++){let a=(o+s*r)*Math.PI/180,l=e.x+n*Math.cos(a),d=e.y+n*Math.sin(a);s===0?i.moveTo(l,d):i.lineTo(l,d);}i.closePath();}function As(i,e){switch(i.kind){case \"backbone\":case \"branch\":return e.defaultStroke;case \"cross-polymer\":return e.crossPolymerBondColor;case \"hbond\":return Ss(i)?e.hbondColor:e.nonCanonicalHbondColor;case \"group\":return e.defaultStroke}}function Ms(i){return Bn}var Ts=[[\"A\",\"T\"],[\"A\",\"U\"],[\"G\",\"C\"]];function Ss(i){if(i.a1.biotype!==b.BASE||i.a2.biotype!==b.BASE)return  false;let e=Qo(i.a1),t=Qo(i.a2);for(let[n,o]of Ts)if(e===n&&t===o||e===o&&t===n)return  true;return  false}function Qo(i){let e=i.monomer?.naturalAnalog,t=e!==void 0&&e!==\"\"?e:i.symbol;return t.length===0?\"\":t.charAt(0).toUpperCase()}function fe(i){let e=new Map,t=new Map;for(let o of i.bonds){let r=o.a1.id,s=o.a2.id,a=t.get(r);a===void 0&&(a=[],t.set(r,a)),a.push(o);let l=t.get(s);l===void 0&&(l=[],t.set(s,l)),l.push(o);}for(let o of i.atoms)ti(e,o,t.get(o.id)??[]);for(let o of i.groups){if(o.kind!==\"bracket\")continue;let r=o.repeat?.min??1;if(r===1)continue;let s=new Set(o.members.map(l=>l.target)),a=new Map;for(let l of i.atoms){if(!s.has(l.bio.chainId))continue;let d=new Map;ti(d,l,t.get(l.id)??[]);for(let[c,u]of d)a.set(c,(a.get(c)??0)+u*(r-1));}for(let[l,d]of a)e.set(l,(e.get(l)??0)+d);}for(let[o,r]of [...e])r===0&&e.delete(o);let n=Ls(e);return {elements:e,mw:n}}var Es={H:1.008,C:12.011,N:14.007,O:15.999,F:18.998,Na:22.99,Mg:24.305,P:30.974,S:32.06,Cl:35.45,K:39.098,Ca:40.078,Br:79.904,I:126.904,Fe:55.845,Zn:65.38,Cu:63.546},Cs={C:4,N:3,O:2,S:2,P:3,F:1,Cl:1,Br:1,I:1,H:1};function Ls(i){let e=0;for(let[t,n]of i){let o=Es[t];o!==void 0&&(e+=o*n);}return Math.round(e*1e3)/1e3}function ti(i,e,t){if(e.monomer===null)return;let n=Rs(e.monomer);for(let[o,r]of n.elements)i.set(o,(i.get(o)??0)+r);for(let o of t){if(o.kind===\"hbond\"||o.kind===\"group\")continue;let r=o.a1.id===e.id?o.r1:o.r2,s=Bs(e.monomer,r);if(s===void 0)continue;let a=oi(s);for(let[l,d]of a)i.set(l,(i.get(l)??0)-d);}}function Bs(i,e){if(e.kind!==\"numeric\"&&e.kind!==\"positional\")return;let t=(e.kind===\"numeric\",e.r);for(let n of i.rgroups){let o=/^R([1-9][0-9]*)$/.exec(n.label);if(o!==null&&parseInt(o[1],10)===t)return n.capGroupName}}function oi(i){let e=new Map;switch(i){case \"H\":e.set(\"H\",1);break;case \"OH\":e.set(\"H\",1),e.set(\"O\",1);break;}return e}var ni=new WeakMap;function Rs(i){let e=ni.get(i);if(e!==void 0)return e;let t=Is(i);return ni.set(i,t),t}function Is(i){let e=new Map;if(i.molfile===void 0||i.molfile===\"\")return {elements:e};let t=Ps(i.molfile);if(t===null)return {elements:e};let{atoms:n,bondOrders:o}=t;for(let r=0;r<n.length;r++){let s=n[r];if(s===\"R\"||s===\"R#\"||s===\"*\")continue;e.set(s,(e.get(s)??0)+1);let a=Cs[s];if(a===void 0)continue;let l=o[r]??0,d=a-l;d>0&&e.set(\"H\",(e.get(\"H\")??0)+d);}for(let r of i.rgroups){let s=r.capGroupName;if(s===void 0)continue;let a=oi(s);for(let[l,d]of a)e.set(l,(e.get(l)??0)+d);}return {elements:e}}function Ps(i){let e=i.split(/\\r\\n|\\n|\\r/);if(e.length<5)return null;let t=e[3];if(t===void 0||t.length<6)return null;let n=parseInt(t.slice(0,3),10),o=parseInt(t.slice(3,6),10);if(!Number.isFinite(n)||!Number.isFinite(o)||e.length<4+n+o)return null;let r=[];for(let a=0;a<n;a++){let l=e[4+a];if(l===void 0)return null;let d=l.slice(31,34).trim();r.push(d);}let s=new Array(n).fill(0);for(let a=0;a<o;a++){let l=e[4+n+a];if(l===void 0)return null;let d=parseInt(l.slice(0,3),10),c=parseInt(l.slice(3,6),10),u=parseInt(l.slice(6,9),10);if(!Number.isFinite(d)||!Number.isFinite(c)||!Number.isFinite(u))continue;let m=u===4?1:u;d>=1&&d<=n&&(s[d-1]=(s[d-1]??0)+m),c>=1&&c<=n&&(s[c-1]=(s[c-1]??0)+m);}return {atoms:r,bondOrders:s}}function Pe(i){return fe(i).mw}var Hn={W:5.5,Y:1.49,C:.0625},Hs={AA:13.65,AC:10.67,AG:12.79,AU:12.14,CA:10.67,CC:7.52,CG:9.39,CU:8.37,GA:12.79,GC:9.39,GG:11.77,GU:10.21,UA:12.14,UC:8.37,UG:10.21,UU:8.99},ii={A:15.4,C:7.4,G:11.7,U:10,T:8.8};function He(i){let e=0;for(let t of i.chains)t.polymerType===\"PEPTIDE\"?e+=$s(t.backboneAtoms):t.polymerType===\"RNA\"&&(e+=Ds(t.backboneAtoms));return Math.round(e*1e4)/1e4}function $s(i){let e=0,t=0,n=0;for(let o of i){let r=ri(o);r===\"W\"?e++:r===\"Y\"?t++:r===\"C\"&&n++;}return Hn.W*e+Hn.Y*t+Hn.C*n}function Ds(i){let e=[];for(let o of i)if(o.branchAtom!==void 0&&o.branchAtom.biotype===b.BASE){let r=ri(o.branchAtom);r===\"T\"&&(r=\"U\"),r!==\"\"&&e.push(r);}if(e.length===0)return 0;if(e.length===1){let o=e[0];return ii[o]??0}let t=0;for(let o=0;o<e.length-1;o++){let r=e[o],s=e[o+1],a=Hs[r+s];a!==void 0&&(t+=a);}let n=0;for(let o=1;o<e.length-1;o++){let r=e[o];n+=ii[r]??0;}return 2*t-n}function ri(i){let e=i.monomer;return e!==null&&e.naturalAnalog!==void 0&&e.naturalAnalog!==\"\"?e.naturalAnalog.charAt(0).toUpperCase():i.symbol===\"\"?\"\":i.symbol.charAt(0).toUpperCase()}function Pt(i){let e=[];e.push(\"HWE pseudo-molfile\"),e.push(\" HWE          2D\"),e.push(\"\");let t=i.atoms.length,n=i.bonds.length;e.push(Os(t,n));for(let r of i.atoms)e.push(Ns(r));let o=new Map;for(let r=0;r<i.atoms.length;r++)o.set(i.atoms[r].id,r+1);for(let r of i.bonds){let s=o.get(r.a1.id),a=o.get(r.a2.id);s===void 0||a===void 0||e.push(Fs(s,a));}return e.push(\"M  END\"),e.join(`\n`)+`\n`}function Os(i,e){return $e(i)+$e(e)+\"  0  0  0  0  0  0  0  0999 V2000\"}function Ns(i){let e=Gs(i);return $n(i.p.x)+$n(i.p.y)+$n(0)+\" \"+Vs(e,3)+\" 0  0  0  0  0  0  0  0  0  0  0  0\"}function Fs(i,e){return $e(i)+$e(e)+$e(1)+$e(0)}function Gs(i){let e=i.monomer;return e!==null&&e.symbol!==\"\"?e.symbol:i.symbol!==\"\"?i.symbol:e!==null&&e.naturalAnalog!==void 0&&e.naturalAnalog!==\"\"?e.naturalAnalog:\"X\"}function $e(i){let e=String(i);return e.length>=3?e:\" \".repeat(3-e.length)+e}function Vs(i,e){return i.length>=e?i:i+\" \".repeat(e-i.length)}function $n(i){let e=i.toFixed(4);return e.length>=10?e.slice(0,10):\" \".repeat(10-e.length)+e}var Us=new Map;function zs(i){return `${i.mode}|${i.resolveMonomers?1:0}|${i.helm}`}function Ks(i){let e=i.chains.map(o=>`${o.id}:${o.polymerType}:${o.backboneAtoms.length}`).join(\",\"),t=i.atoms.map(o=>`${o.id}@${o.symbol}@${o.bio.chainId}`).join(\";\"),n=i.bonds.map(o=>`${o.id}:${o.a1.id}-${o.a2.id}:${o.kind}`).join(\";\");return `${e}#${t}#${n}`}var Ws=256,Dn=class{constructor(e){this._destroyed=false;this._parseHits=0;this._parseMisses=0;this._layoutHits=0;this._layoutMisses=0;this._renderHits=0;this._renderMisses=0;if(e.monomerLib===void 0||e.monomerLib===null)throw new TypeError(\"HelmService: options.monomerLib is required\");this.monomerLib=e.monomerLib,this.theme=e.theme??H,this.logger=e.logger??new Se,this.options=Object.freeze({...e});let t=e.cacheSize??Ws;this._parseCache=new Te({max:t}),this._layoutCache=new Te({max:t}),this._renderCache=new Te({max:t}),this._libUnsub=this.monomerLib.onChanged.subscribe(()=>{this.clearCaches();});}parse(e,t){this._ensureLive(),e=this._normalizeHelm(e);let n=t?.mode??\"lenient\",o=t?.resolveMonomers!==false,r=zs({mode:n,resolveMonomers:o,helm:e}),s=this._parseCache.get(r);if(s!==void 0)return this._parseHits+=1,s;this._parseMisses+=1;let a={mode:n,resolveMonomers:o},l=et(e,this.monomerLib,a),d={mol:l.mol,diagnostics:Object.freeze([...l.diagnostics])};return this._parseCache.set(r,d),d}serialize(e,t){this._ensureLive();let n={...t?.canonicalize!==void 0?{canonicalize:t.canonicalize}:{},...t?.includeHighlights!==void 0?{includeHighlights:t.includeHighlights}:{},...t?.version!==void 0?{version:t.version}:{}};return Re(e,n)}validate(e,t){this._ensureLive(),e=this._normalizeHelm(e);let{mol:n,diagnostics:o}=this.parse(e,{mode:\"lenient\"}),r=t?.mode!==void 0?{mode:t.mode}:{},s=yn(n,this.monomerLib,r);return [...o,...s]}canonicalize(e){this._ensureLive(),e=this._normalizeHelm(e);let{mol:t}=this.parse(e,{mode:\"lenient\"}),n=fn(t);return Re(n,{canonicalize:true,version:\"V2.0\"})}removeGaps(e){return this._ensureLive(),bn(this._normalizeHelm(e),this.monomerLib)}renderToSvg(e,t){this._ensureLive(),e=this._normalizeHelm(e);let n=this._resolveRenderOptions(t),o=this._renderKey(e,n),r=this._renderCache.get(o);if(r!==void 0)return this._renderHits+=1,r;this._renderMisses+=1;let{mol:s}=this.parse(e,{mode:\"lenient\"}),a=this._layout(s,n.bondLength),{svg:l}=Rt(a,n);return this._renderCache.set(o,l),l}renderMol(e,t){this._ensureLive();let n=this._resolveRenderOptions(t),{svg:o}=Rt(e,n);return o}renderMolResult(e,t){this._ensureLive();let n=this._resolveRenderOptions(t);return Rt(e,n)}async renderToPng(e,t){if(this._ensureLive(),e=this._normalizeHelm(e),typeof globalThis.OffscreenCanvas!=\"function\")throw new j(\"png-rendering-requires-browser\",\"HelmService.renderToPng requires OffscreenCanvas (browser-only).\");let n=this._resolveRenderOptions(t),{mol:o}=this.parse(e,{mode:\"lenient\"}),r=this._layout(o,n.bondLength);return ei(r,n)}renderToCanvas(e,t,n,o){this._ensureLive(),t=this._normalizeHelm(t);let r=this._resolveRenderOptions(o),{mol:s}=this.parse(t,{mode:\"lenient\"}),a=this._layout(s,r.bondLength),{bbox:l,drawBox:d}=It(e,a,n,r);return {mol:a,bbox:l,drawBox:d}}renderMolToCanvas(e,t,n,o){this._ensureLive();let r=this._resolveRenderOptions(o),{bbox:s,drawBox:a}=It(e,t,n,r);return {mol:t,bbox:s,drawBox:a}}*renderMany(e,t){for(let n of e??[]){let o=this.renderToSvg(n.helm,t);yield {id:n.id,svg:o};}}getFormula(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:\"lenient\"});return fe(t)}getMolWeight(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:\"lenient\"});return Pe(t)}getExtinctionCoefficient(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:\"lenient\"});return He(t)}getMolfile(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:\"lenient\"});return Pt(t)}hasAtomicMolfileProvider(){return typeof this.options.atomicMolfileProvider==\"function\"}async getAtomicMolfile(e){this._ensureLive(),e=this._normalizeHelm(e);let t=this.options.atomicMolfileProvider;if(typeof t!=\"function\")throw new j(\"atomic-molfile-not-configured\",\"Set HelmServiceOptions.atomicMolfileProvider to enable atomic-level expansion.\");return await t(e,this.monomerLib)}hasExtraPanes(){let e=this.options.extraPanes;return e!==void 0&&e.size>0}getExtraPanes(){return this.options.extraPanes??Us}invalidate(e){if(e===void 0){this.clearCaches();return}for(let t of [this._parseCache,this._layoutCache,this._renderCache]){let n=[];for(let o of t.keys())e(o)&&n.push(o);for(let o of n)t.delete(o);}}clearCaches(){this._parseCache.clear(),this._layoutCache.clear(),this._renderCache.clear(),this._parseHits=0,this._parseMisses=0,this._layoutHits=0,this._layoutMisses=0,this._renderHits=0,this._renderMisses=0;}destroy(){this._destroyed||(this._destroyed=true,this._libUnsub(),this.clearCaches());}_ensureLive(){if(this._destroyed)throw new j(\"service-destroyed\",\"HelmService instance has been destroyed.\")}_normalizeHelm(e){return e==null?\"\":typeof e==\"string\"?e:String(e)}_resolveRenderOptions(e){let t={},n=e?.theme??this.theme;return t.theme=n,e?.width!==void 0&&(t.width=e.width),e?.height!==void 0&&(t.height=e.height),e?.backColor!==void 0&&(t.backColor=e.backColor),e?.padding!==void 0&&(t.padding=e.padding),e?.showIds!==void 0&&(t.showIds=e.showIds),e?.showAnnotations!==void 0&&(t.showAnnotations=e.showAnnotations),e?.bondLength!==void 0&&(t.bondLength=e.bondLength),e?.fontSize!==void 0&&(t.fontSize=e.fontSize),e?.maxScale!==void 0&&(t.maxScale=e.maxScale),e?.showRGroupLabels!==void 0&&(t.showRGroupLabels=e.showRGroupLabels),e?.selectedAtomIds!==void 0&&(t.selectedAtomIds=e.selectedAtomIds),e?.highlightedAtomIds!==void 0&&(t.highlightedAtomIds=e.highlightedAtomIds),e?.fixedModelBbox!==void 0&&(t.fixedModelBbox=e.fixedModelBbox),t}_renderKey(e,t){let o=(t.theme??this.theme).name,r=this._libCacheTag(),s=t.width??0,a=t.height??0,l=t.padding??-1,d=t.bondLength??-1,c=t.backColor??\"\",u=t.showIds===true?1:0,m=t.showAnnotations===false?0:1,p=t.maxScale??1;return `${r}|${o}|${s}x${a}|p${l}|b${d}|bg${c}|i${u}a${m}|s${p}|${e}`}_layout(e,t){let n=Ks(e),o=`${this._libCacheTag()}|${t??\"d\"}|${n}`,r=this._layoutCache.get(o);if(r!==void 0)return this._layoutHits+=1,r;this._layoutMisses+=1;let s=t!==void 0?ne(e,{bondLength:t}):ne(e);return this._layoutCache.set(o,s),s}get stats(){return {parseHits:this._parseHits,parseMisses:this._parseMisses,layoutHits:this._layoutHits,layoutMisses:this._layoutMisses,renderHits:this._renderHits,renderMisses:this._renderMisses}}_libCacheTag(){let e=this.monomerLib,t=typeof e.version==\"number\"?e.version:0;return `${this.monomerLib.source}@${t}`}};var Q=class{constructor(e,t){this.atoms=e,this.bonds=t,this.isEmpty=e.size===0&&t.size===0,Object.freeze(this);}},si=new Q(new Set,new Set),G={empty(){return si},fromAtoms(i){return new Q(new Set(i),new Set)},fromBonds(i){return new Q(new Set,new Set(i))},fromAtomsAndBonds(i,e){return new Q(new Set(i),new Set(e))},union(...i){if(i.length===0)return si;let e=new Set,t=new Set;for(let n of i){for(let o of n.atoms)e.add(o);for(let o of n.bonds)t.add(o);}return new Q(e,t)},difference(i,e){let t=new Set,n=new Set;for(let o of i.atoms)e.atoms.has(o)||t.add(o);for(let o of i.bonds)e.bonds.has(o)||n.add(o);return new Q(t,n)},intersect(i,e){let t=new Set,n=new Set;for(let o of i.atoms)e.atoms.has(o)&&t.add(o);for(let o of i.bonds)e.bonds.has(o)&&n.add(o);return new Q(t,n)},toggle(i,e){if(e.kind===\"atom\"){let n=new Set(i.atoms);return n.has(e.id)?n.delete(e.id):n.add(e.id),new Q(n,new Set(i.bonds))}let t=new Set(i.bonds);return t.has(e.id)?t.delete(e.id):t.add(e.id),new Q(new Set(i.atoms),t)},hasAtom(i,e){return i.atoms.has(e)},hasBond(i,e){return i.bonds.has(e)},equals(i,e){if(i===e)return  true;if(i.atoms.size!==e.atoms.size||i.bonds.size!==e.bonds.size)return  false;for(let t of i.atoms)if(!e.atoms.has(t))return  false;for(let t of i.bonds)if(!e.bonds.has(t))return  false;return  true}};function be(i){let e=i.monomer;return e===null?0:e.rgroups.length}function ai(i,e){let t=new Set;for(let r of e)r.a1.id===i.id&&r.r1.kind===\"numeric\"&&t.add(r.r1.r),r.a2.id===i.id&&r.r2.kind===\"numeric\"&&t.add(r.r2.r);let n=[],o=Array.from(t).sort((r,s)=>r-s);for(let r of o)n.push(r);return n}function W(i,e){let t=be(i);if(t===0)return [];let n=new Set(ai(i,e)),o=[];for(let r=1;r<=t;r++)n.has(r)||o.push(r);return o}function js(i,e){return W(i,e).length>0}function Ht(i,e){let t=[];for(let n of e)if(n.a1.id===i.id){let o=n.r1.kind===\"numeric\"?n.r1.r:0;t.push({bond:n,side:\"r1\",rNumber:o});}else if(n.a2.id===i.id){let o=n.r2.kind===\"numeric\"?n.r2.r:0;t.push({bond:n,side:\"r2\",rNumber:o});}return t}function qs(i){switch(i){case b.AA:return v.PEPTIDE;case b.SUGAR:case b.BASE:case b.LINKER:case b.NUCLEOTIDE:return v.RNA;case b.CHEM:return v.CHEM;case b.BLOB:return v.BLOB}}function Ys(i){switch(i){case v.PEPTIDE:return \"PEPTIDE\";case v.RNA:return \"RNA\";case v.CHEM:return \"CHEM\";case v.BLOB:return \"BLOB\";case v.G:return \"G\"}}function Xs(i){let e=0;for(let t of i.atoms)t.id>e&&(e=t.id);for(let t of i.bonds)t.id>e&&(e=t.id);return e}function $t(i,e){return i.kind!==e.kind?false:i.kind===\"numeric\"&&e.kind===\"numeric\"?i.r===e.r:i.kind===\"positional\"&&e.kind===\"positional\"?i.position===e.position&&i.r===e.r:true}var O=class{constructor(e){this._atoms=new Map;this._atomOrder=[];this._bonds=new Map;this._bondOrder=[];this._chains=new Map;this._chainOrder=[];this._addedAtoms=new Set;this._removedAtoms=new Set;this._modifiedAtoms=new Set;this._addedBonds=new Set;this._removedBonds=new Set;this._modifiedBonds=new Set;this._topologyDirty=false;this._idgen=new _e;let t=Xs(e);for(let n=0;n<t;n++)this._idgen.next();for(let n of e.chains)this._chains.set(n.id,{id:n.id,polymerType:n.polymerType,backboneAtomIds:n.backboneAtoms.map(o=>o.id),bondIds:n.bonds.map(o=>o.id),annotation:n.annotation}),this._chainOrder.push(n.id);for(let n of e.atoms)this._atoms.set(n.id,{id:n.id,p:{x:n.p.x,y:n.p.y},biotype:n.biotype,symbol:n.symbol,monomer:n.monomer,bio:{...n.bio},hidden:n.hidden,selected:n.selected,highlighted:n.highlighted,tag:n.tag,branchAtomId:n.branchAtom?.id,inlineSource:n.inlineSource}),this._atomOrder.push(n.id);for(let n of e.bonds)this._bonds.set(n.id,{id:n.id,a1Id:n.a1.id,a2Id:n.a2.id,kind:n.kind,r1:n.r1,r2:n.r2,ratio:n.ratio,tag:n.tag}),this._bondOrder.push(n.id);this._groups=[...e.groups],this._annotations=e.annotations;}addAtom(e){let t=this._idgen.next(),n=qs(e.biotype),o=e.chainId??this._pickChainId(n),r=this._chains.get(o);r===void 0&&(r={id:o,polymerType:n,backboneAtomIds:[],bondIds:[],annotation:void 0},this._chains.set(o,r),this._chainOrder.push(o));let s=e.positionInChain??r.backboneAtomIds.length+1,a={id:t,p:{x:e.p.x,y:e.p.y},biotype:e.biotype,symbol:e.symbol,monomer:null,bio:{chainId:o,positionInChain:s,continuousId:0},hidden:false,selected:false,highlighted:false,tag:void 0,branchAtomId:void 0,inlineSource:void 0};this._atoms.set(t,a),this._atomOrder.push(t);let l=Math.max(0,Math.min(s-1,r.backboneAtomIds.length));return r.backboneAtomIds.splice(l,0,t),this._addedAtoms.add(t),this._topologyDirty=true,t}removeAtom(e){let t=this._atoms.get(e);if(t===void 0)return;let n=[];for(let s of this._bonds.values())(s.a1Id===e||s.a2Id===e)&&n.push(s.id);for(let s of n)this._removeBondInternal(s);for(let s of this._atoms.values())s.branchAtomId===e&&(s.branchAtomId=void 0);let o=this._chains.get(t.bio.chainId);if(o!==void 0){let s=o.backboneAtomIds.indexOf(e);s>=0&&o.backboneAtomIds.splice(s,1);}this._atoms.delete(e);let r=this._atomOrder.indexOf(e);r>=0&&this._atomOrder.splice(r,1),this._addedAtoms.has(e)?this._addedAtoms.delete(e):this._removedAtoms.add(e),this._modifiedAtoms.delete(e),this._topologyDirty=true;}updateAtom(e,t){let n=this._atoms.get(e);n!==void 0&&(t.p!==void 0&&(n.p={x:t.p.x,y:t.p.y}),t.symbol!==void 0&&(n.symbol=t.symbol),t.selected!==void 0&&(n.selected=t.selected),t.highlighted!==void 0&&(n.highlighted=t.highlighted),\"tag\"in t&&(n.tag=t.tag),t.hidden!==void 0&&(n.hidden=t.hidden),this._addedAtoms.has(e)||this._modifiedAtoms.add(e));}addBond(e){if(!this._atoms.has(e.a1))throw new Error(`Transaction.addBond: atom ${e.a1} does not exist`);if(!this._atoms.has(e.a2))throw new Error(`Transaction.addBond: atom ${e.a2} does not exist`);for(let r of this._bonds.values()){let s=r.a1Id===e.a1&&r.a2Id===e.a2&&$t(r.r1,e.r1)&&$t(r.r2,e.r2),a=r.a1Id===e.a2&&r.a2Id===e.a1&&$t(r.r1,e.r2)&&$t(r.r2,e.r1);if(s||a)throw new Error(`Transaction.addBond: duplicate bond ${e.a1}:${li(e.r1)}-${e.a2}:${li(e.r2)}`)}let t=this._idgen.next();this._bonds.set(t,{id:t,a1Id:e.a1,a2Id:e.a2,kind:e.kind,r1:e.r1,r2:e.r2,ratio:void 0,tag:void 0}),this._bondOrder.push(t);let n=this._atoms.get(e.a1),o=this._atoms.get(e.a2);if(n!==void 0&&o!==void 0&&n.bio.chainId===o.bio.chainId){let r=this._chains.get(n.bio.chainId);r!==void 0&&r.bondIds.push(t);}return this._addedBonds.add(t),this._topologyDirty=true,t}removeBond(e){this._bonds.has(e)&&(this._removeBondInternal(e),this._topologyDirty=true);}updateBond(e,t){let n=this._bonds.get(e);n!==void 0&&(\"tag\"in t&&(n.tag=t.tag),\"ratio\"in t&&(n.ratio=t.ratio),this._addedBonds.has(e)||this._modifiedBonds.add(e));}commit(){let e=new Map;for(let l of this._atomOrder){let d=this._atoms.get(l);if(d===void 0)continue;let c={id:d.id,p:{x:d.p.x,y:d.p.y},biotype:d.biotype,symbol:d.symbol,monomer:d.monomer,bio:{...d.bio},hidden:d.hidden,selected:d.selected,highlighted:d.highlighted,...d.tag!==void 0?{tag:d.tag}:{},...d.inlineSource!==void 0?{inlineSource:d.inlineSource}:{}};e.set(l,c);}for(let l of this._atomOrder){let d=this._atoms.get(l);if(d===void 0||d.branchAtomId===void 0)continue;let c=e.get(l),u=e.get(d.branchAtomId);c===void 0||u===void 0||(c.branchAtom=u);}let t=new Map;for(let l of this._bondOrder){let d=this._bonds.get(l);if(d===void 0)continue;let c=e.get(d.a1Id),u=e.get(d.a2Id);if(c===void 0||u===void 0)continue;let m={id:d.id,a1:c,a2:u,kind:d.kind,r1:d.r1,r2:d.r2,...d.ratio!==void 0?{ratio:{...d.ratio}}:{},...d.tag!==void 0?{tag:d.tag}:{}};t.set(l,m);}let n=[];for(let l of this._chainOrder){let d=this._chains.get(l);if(d===void 0||d.backboneAtomIds.length===0&&d.bondIds.length===0)continue;let c=[];for(let m of d.backboneAtomIds){let p=e.get(m);p!==void 0&&c.push(p);}let u=[];for(let m of d.bondIds){let p=t.get(m);p!==void 0&&u.push(p);}n.push({id:d.id,polymerType:d.polymerType,backboneAtoms:c,bonds:u,...d.annotation!==void 0?{annotation:d.annotation}:{}});}let o=this._atomOrder.map(l=>e.get(l)).filter(l=>l!==void 0),r=this._bondOrder.map(l=>t.get(l)).filter(l=>l!==void 0),s={atoms:o,bonds:r,chains:n,groups:[...this._groups],annotations:this._annotations};this._topologyDirty&&(s=Js(s));let a=Object.freeze({addedAtomIds:new Set(this._addedAtoms),removedAtomIds:new Set(this._removedAtoms),addedBondIds:new Set(this._addedBonds),removedBondIds:new Set(this._removedBonds),modifiedAtomIds:new Set(this._modifiedAtoms),modifiedBondIds:new Set(this._modifiedBonds)});return this._addedAtoms.clear(),this._removedAtoms.clear(),this._modifiedAtoms.clear(),this._addedBonds.clear(),this._removedBonds.clear(),this._modifiedBonds.clear(),this._topologyDirty=false,{mol:s,changes:a}}_removeBondInternal(e){if(this._bonds.get(e)===void 0)return;this._bonds.delete(e);let n=this._bondOrder.indexOf(e);n>=0&&this._bondOrder.splice(n,1);for(let o of this._chains.values()){let r=o.bondIds.indexOf(e);r>=0&&o.bondIds.splice(r,1);}this._addedBonds.has(e)?this._addedBonds.delete(e):this._removedBonds.add(e),this._modifiedBonds.delete(e);}_pickChainId(e){let t=Ys(e),n=1;for(;this._chains.has(`${t}${n}`);)n+=1;return `${t}${n}`}};function li(i){switch(i.kind){case \"numeric\":return `R${i.r}`;case \"unspecified\":return \"?\";case \"wildcard\":return \"*\";case \"pair\":return \"pair\";case \"positional\":return `${i.position}pos:R${i.r}`}}function Js(i){let e=Ee(i),t=new Map;for(let a of i.atoms){let l=e.get(a.id);if(l===void 0||l===a.bio.continuousId){t.set(a.id,a);continue}t.set(a.id,{...a,bio:{...a.bio,continuousId:l}});}for(let a of i.atoms){if(a.branchAtom===void 0)continue;let l=t.get(a.id),d=t.get(a.branchAtom.id);l===void 0||d===void 0||(l.branchAtom=d);}let n=i.bonds.map(a=>{let l=t.get(a.a1.id),d=t.get(a.a2.id);return l===void 0||d===void 0||l===a.a1&&d===a.a2?a:{...a,a1:l,a2:d}}),o=new Map;for(let a of n)o.set(a.id,a);let r=i.chains.map(a=>{let l=[];for(let c of a.backboneAtoms)l.push(t.get(c.id)??c);let d=[];for(let c of a.bonds)d.push(o.get(c.id)??c);return {id:a.id,polymerType:a.polymerType,backboneAtoms:l,bonds:d,...a.annotation!==void 0?{annotation:a.annotation}:{}}});return {atoms:i.atoms.map(a=>t.get(a.id)??a),bonds:n,chains:r,groups:i.groups,annotations:i.annotations}}var q=class{constructor(e,t,n){this.atoms=[];this.bonds=[];this.bondHitWidth=n?.bondHitWidth??4,this.rebuild(e,t);}rebuild(e,t){let n=[];for(let r of e.atoms)r.hidden||n.push({atom:r,bbox:pe(r,t),hitRadius:qo(r,t)});let o=[];for(let r of e.bonds)o.push({bond:r,a:r.a1.p,b:r.a2.p});this.atoms=n,this.bonds=o;}test(e){let t=null,n=null;for(let r of this.atoms){if(!Dt(e,r.bbox))continue;let s=e.x-r.atom.p.x,a=e.y-r.atom.p.y,l=Math.sqrt(s*s+a*a);l>r.hitRadius||(t===null||l<t.d?(n=t,t={entry:r,d:l}):(n===null||l<n.d)&&(n={entry:r,d:l}));}if(t!==null)return {atom:t.entry.atom};let o=null;for(let r of this.bonds){let s=Zs(e,r.a,r.b);s>this.bondHitWidth||(o===null||s<o.d)&&(o={entry:r,d:s});}return o!==null?{bond:o.entry.bond}:null}testRect(e){let t=[];for(let o of this.atoms)Dt(o.atom.p,e)&&t.push(o.atom);let n=[];for(let o of this.bonds)Dt(o.a,e)&&Dt(o.b,e)&&n.push(o.bond);return {atoms:t,bonds:n}}atomCount(){return this.atoms.length}bondCount(){return this.bonds.length}};function Dt(i,e){return i.x>=e.x&&i.x<=e.x+e.width&&i.y>=e.y&&i.y<=e.y+e.height}function Zs(i,e,t){let n=t.x-e.x,o=t.y-e.y,r=n*n+o*o;if(r===0){let u=i.x-e.x,m=i.y-e.y;return Math.sqrt(u*u+m*m)}let 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n=Math.min(e.x,t.x),o=Math.min(e.y,t.y),r=Math.abs(e.x-t.x),s=Math.abs(e.y-t.y);this._paintSelectionRectAt(n,o,r,s);}_paintSelectionRectFromRect(e){this._paintSelectionRectAt(e.x,e.y,e.width,e.height);}_paintSelectionRectAt(e,t,n,o){let r=\"http://www.w3.org/2000/svg\",s=this._svgRoot.querySelector(\".hw-content\");if(s===null)return;let a=s.querySelector(\".hw-selection-rect\");a===null&&(a=this._doc.createElementNS(r,\"rect\"),a.setAttribute(\"class\",\"hw-selection-rect\"),a.setAttribute(\"data-testid\",\"selection-rect\"),a.setAttribute(\"fill\",\"rgba(31, 95, 205, 0.08)\"),a.setAttribute(\"stroke\",\"#1f5fcd\"),a.setAttribute(\"stroke-width\",\"1\"),a.setAttribute(\"stroke-dasharray\",\"4 3\"),a.setAttribute(\"pointer-events\",\"none\"),s.appendChild(a)),a.setAttribute(\"x\",String(e)),a.setAttribute(\"y\",String(t)),a.setAttribute(\"width\",String(n)),a.setAttribute(\"height\",String(o));}_clearSelectionRect(){let e=this._svgRoot.querySelector(\".hw-selection-rect\");e!==null&&e.parentNode!==null&&e.parentNode.removeChild(e);}};Ft._RDKIT_CACHE_LIMIT=256;var Nt=Ft;function pi(i){switch(i.kind){case \"numeric\":return `R${i.r}`;case \"unspecified\":return \"?\";case \"wildcard\":return \"*\";case \"pair\":return \"pair\";case \"positional\":return `${i.position}pos:R${i.r}`}}var ie=class ie{constructor(e,t){this._onClose=null;this._primaryAction=null;this._host=e,this._doc=t.documentImpl??S(e);let n=this._doc,o={class:\"hw-modal-backdrop\",role:\"presentation\"};t.testId!==void 0&&(o[\"data-testid\"]=`dialog-${t.testId}`);let r=g(n,\"div\",o),s={class:\"hw-modal\",role:\"dialog\",\"aria-modal\":\"true\",\"aria-label\":t.title};t.testId!==void 0&&(s[\"data-testid\"]=`dialog-${t.testId}-frame`);let a=g(n,\"div\",s),l=g(n,\"div\",{class:\"hw-modal__header\"},[t.title]),d=g(n,\"div\",{class:\"hw-modal__body\"});a.appendChild(l),a.appendChild(d),r.appendChild(a);let c=u=>{u.stopPropagation();};for(let u of [\"mousedown\",\"mousemove\",\"mouseup\",\"mouseover\",\"mouseenter\",\"mouseleave\",\"wheel\",\"contextmenu\",\"dblclick\",\"keydown\",\"keyup\",\"keypress\"])r.addEventListener(u,c);a.addEventListener(\"keydown\",u=>{let m=u;if(m.key!==\"Enter\"||m.target?.tagName===\"TEXTAREA\")return;let p=this._primaryAction;p!==null&&(m.preventDefault?.(),m.stopImmediatePropagation?.(),p());}),r.addEventListener(\"click\",u=>{if(u.target===r){this.close();return}u.stopPropagation();}),this.root=r,this.body=d;}static anyOpen(){return ie._openStack.length>0}static closeTopmost(){let e=ie._openStack[ie._openStack.length-1];return e===void 0?false:(e.close(),true)}open(e){this._onClose=e??null,this.root.parentNode===null&&this._host.appendChild(this.root),ie._openStack.includes(this)||ie._openStack.push(this),Ot(this._doc);}close(){let e=ie._openStack.indexOf(this);e>=0&&ie._openStack.splice(e,1),this.root.parentNode!==null&&this.root.parentNode.removeChild(this.root);let t=this._onClose;this._onClose=null,t!==null&&t();}setPrimaryAction(e){this._primaryAction=e;}get isOpen(){return this.root.parentNode!==null}};ie._openStack=[];var X=ie;function Ne(i,e,t,n){let o=`hw-input-${Math.random().toString(36).slice(2,9)}`,r=g(i,\"label\",{for:o,class:\"hw-modal__label\"},[e]),s=i.createElement(\"input\");return s.setAttribute(\"id\",o),s.setAttribute(\"type\",\"text\"),s.setAttribute(\"class\",\"hw-modal__input\"),n!==void 0&&s.setAttribute(\"data-testid\",n),s.value=t,{row:g(i,\"div\",{class:\"hw-modal__row\"},[r,s]),input:s}}function Fe(i,e,t,n,o){let r=`hw-sel-${Math.random().toString(36).slice(2,9)}`,s=g(i,\"label\",{for:r,class:\"hw-modal__label\"},[e]),a=i.createElement(\"select\");a.setAttribute(\"id\",r),a.setAttribute(\"class\",\"hw-modal__select\"),o!==void 0&&a.setAttribute(\"data-testid\",o);for(let d of t){let c=i.createElement(\"option\");c.setAttribute(\"value\",d.value),d.value===n&&c.setAttribute(\"selected\",\"\"),c.appendChild(i.createTextNode(d.label)),a.appendChild(c);}return {row:g(i,\"div\",{class:\"hw-modal__row\"},[s,a]),select:a}}function Ge(i,e){let t=i.createElement(\"button\");t.setAttribute(\"class\",\"hw-modal__ok\"),t.setAttribute(\"type\",\"button\"),e!==void 0&&t.setAttribute(\"data-testid\",`${e}-ok`),t.appendChild(i.createTextNode(\"OK\"));let n=i.createElement(\"button\");return n.setAttribute(\"class\",\"hw-modal__cancel\"),n.setAttribute(\"type\",\"button\"),e!==void 0&&n.setAttribute(\"data-testid\",`${e}-cancel`),n.appendChild(i.createTextNode(\"Cancel\")),{row:g(i,\"div\",{class:\"hw-modal__actions\"},[t,n]),ok:t,cancel:n}}var Ve=class{constructor(e,t){this._modal=null;this._editor=e;let n=e._getHost();if(n===null)throw new Error(\"ChooseRDialog: editor has no host element.\");this._doc=t?.documentImpl??S(n);}open(e,t,n){this.close();let o=this._editor._getHost();if(o===null)return Promise.resolve(null);let r=new X(o,{documentImpl:this._doc,title:\"Choose R-Groups\",testId:\"choose-r\"});this._modal=r;let s=fi(e,n?.freeR1,n?.currentR1,this._editor),a=fi(t,n?.freeR2,n?.currentR2,this._editor),l=g(this._doc,\"div\",{class:\"hw-modal__info\"},[`${e.symbol} (${e.bio.chainId})`]),d=n?.currentR1!==void 0?String(n.currentR1):s[0]?.value??\"1\",c=n?.currentR2!==void 0?String(n.currentR2):a[0]?.value??\"1\",u=Fe(this._doc,\"R-group on side A\",s,d,\"choose-r-r1\"),m=g(this._doc,\"div\",{class:\"hw-modal__info\"},[`${t.symbol} (${t.bio.chainId})`]),p=Fe(this._doc,\"R-group on side B\",a,c,\"choose-r-r2\"),h=Ge(this._doc,\"choose-r\"),f=[];return s.length===0&&f.push(g(this._doc,\"div\",{class:\"hw-modal__info hw-modal__note-fully-booked\"},[`All R-groups on ${e.symbol} are in use.`])),a.length===0&&f.push(g(this._doc,\"div\",{class:\"hw-modal__info hw-modal__note-fully-booked\"},[`All R-groups on ${t.symbol} are in use.`])),new 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o=i.monomer?.rgroups;if(o===void 0||o.length===0)return [{value:\"1\",label:\"R1\"},{value:\"2\",label:\"R2\"},{value:\"3\",label:\"R3\"}];let r;if(e!==void 0)r=new Set(e);else if(r=new Set(W(i,n.getMol().bonds)),r.size===0)for(let l=1;l<=o.length;l++)r.add(l);t!==void 0&&t>=1&&t<=o.length&&r.add(t);let s=[],a=Array.from(r).sort((l,d)=>l-d);for(let l of a){let d=o[l-1];if(d===void 0)continue;let c=d.capGroupName!==void 0&&d.capGroupName!==\"\"?` (${d.capGroupName})`:\"\";s.push({value:String(l),label:`${d.label}${c}`});}return s}var bi=\"next-add-cursor\",ot=28,Gt=ot*2;function yi(i){let e=\"data-testid\";for(let n=0;n<i.body.children.length;n++){let o=i.body.children[n];if(o!==void 0&&o.getAttribute(e)===bi)return o}let t=i.createElement(\"div\");return t.className=\"hw-next-add-cursor\",t.setAttribute(e,bi),t.style.display=\"none\",i.body.appendChild(t),t}function gi(i,e,t,n,o,r,s){let l=Ie({p:{x:0,y:0},biotype:t,symbol:e},o),c=$(n,t,o.colorTheme).background,u=wt(c),m=e.length,p=m<=1?1:Math.min(1,2/m),h=o.fontSize*p,f=`<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"${-ot} ${-ot} ${Gt} ${Gt}\" width=\"${Gt}\" height=\"${Gt}\" class=\"hw-next-add-cursor__svg\" aria-hidden=\"true\"><path d=\"${l}\" fill=\"${c}\" stroke=\"${c}\" stroke-width=\"5\" stroke-linejoin=\"round\" stroke-linecap=\"round\"/><text x=\"0\" y=\"0\" text-anchor=\"middle\" dominant-baseline=\"central\" font-family=\"Helvetica Neue, Helvetica, Arial, sans-serif\" font-size=\"${h}\" fill=\"${u}\">${Qs(e)}</text></svg>`;i.innerHTML=f;let y=i.style;y.left=`${r-ot}px`,y.top=`${s-ot}px`,y.display=\"block\";}function it(i){i!==null&&(i.style.display=\"none\");}function Qs(i){let e=\"\";for(let t=0;t<i.length;t++){let n=i.charAt(t);n===\"<\"?e+=\"&lt;\":n===\">\"?e+=\"&gt;\":n===\"&\"?e+=\"&amp;\":e+=n;}return e}var Vt=class{constructor(e,t,n){this._hoverAtom=null;this._hoverBond=null;this._dragOrigin=null;this._bondStart=null;this._bondDragMoved=false;this._rectDragHappened=false;this._chooseRDialog=null;this._panStart=null;this._atomDragState=null;this._panMoved=false;this._atomDragMoved=false;this._nextAddCursorEl=null;this._destroyed=false;this._unsubs=[];this._host=e,this._editor=t,this._enableContextMenu=n?.enableContextMenu??true,this._tester=new q(t.getMol(),t._currentTheme()),this._unsubs.push(t.on(\"mol:changed\",()=>{this._tester=new q(this._editor.getMol(),this._editor._currentTheme()),this._hoverAtom=null,this._hoverBond=null;})),this._unsubs.push(t.on(\"option:change\",o=>{(o.key===\"mode\"||o.key===\"nextAdd\")&&it(this._nextAddCursorEl);})),this._onMove=o=>this._handleMove(o),this._onClick=o=>this._handleClick(o),this._onDblClick=o=>this._handleDblClick(o),this._onContextMenu=o=>this._handleContextMenu(o),this._onMouseDown=o=>this._handleMouseDown(o),this._onMouseUp=o=>this._handleMouseUp(o),this._onMouseLeave=o=>this._handleMouseLeave(o),this._onWheel=o=>this._handleWheel(o),e.addEventListener(\"mousemove\",this._onMove),e.addEventListener(\"click\",this._onClick),e.addEventListener(\"dblclick\",this._onDblClick),e.addEventListener(\"contextmenu\",this._onContextMenu),e.addEventListener(\"mousedown\",this._onMouseDown),e.addEventListener(\"mouseup\",this._onMouseUp),e.addEventListener(\"mouseleave\",this._onMouseLeave),e.addEventListener(\"wheel\",this._onWheel,{passive:false});}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this._host.removeEventListener(\"mousemove\",this._onMove),this._host.removeEventListener(\"click\",this._onClick),this._host.removeEventListener(\"dblclick\",this._onDblClick),this._host.removeEventListener(\"contextmenu\",this._onContextMenu),this._host.removeEventListener(\"mousedown\",this._onMouseDown),this._host.removeEventListener(\"mouseup\",this._onMouseUp),this._host.removeEventListener(\"mouseleave\",this._onMouseLeave),this._host.removeEventListener(\"wheel\",this._onWheel),this._chooseRDialog!==null&&(this._chooseRDialog.close(),this._chooseRDialog=null),it(this._nextAddCursorEl),this._nextAddCursorEl=null;}}_handleMove(e){if(this._panStart!==null){let s=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),a=s.x-this._panStart.origin.x,l=s.y-this._panStart.origin.y;this._editor.panTo({x:this._panStart.initialOffset.x+a,y:this._panStart.initialOffset.y+l}),this._panMoved=true;return}if(this._atomDragState!==null){let s=this._toModel(e),a=s.x-this._atomDragState.pointerDownModel.x,l=s.y-this._atomDragState.pointerDownModel.y,d=[];for(let c of this._atomDragState.atomIds){let u=this._atomDragState.initialPositions.get(c);u!==void 0&&d.push({atomId:c,p:{x:u.x+a,y:u.y+l}});}this._editor.moveAtoms(d),this._atomDragMoved=true;return}let t=this._toModel(e),n=this._tester.test(t),o=n?.atom??null,r=n?.bond??null;if(this._bondStart!==null){this._bondDragMoved=true;let s=o!==null&&o.id!==this._bondStart.id?o:null;this._editor.fire(\"bond:preview\",{start:this._bondStart,cursor:t,candidate:s,kind:this._editor.getMode()===\"hbond\"?\"hbond\":\"backbone\"});}if(this._hoverAtom!==null&&(o===null||o.id!==this._hoverAtom.id)&&(this._editor.fire(\"monomer:hover-end\",{atom:this._hoverAtom}),this._hoverAtom=null),o!==null&&(this._hoverAtom===null||this._hoverAtom.id!==o.id)&&(this._hoverAtom=o,this._editor.fire(\"monomer:hover\",{atom:o,clientX:e.clientX,clientY:e.clientY,modelX:t.x,modelY:t.y})),this._hoverBond!==null&&(r===null||r.id!==this._hoverBond.id)&&(this._editor.fire(\"bond:hover-end\",{bond:this._hoverBond}),this._hoverBond=null),r!==null&&(this._hoverBond===null||this._hoverBond.id!==r.id)&&(this._hoverBond=r,this._editor.fire(\"bond:hover\",{bond:r,clientX:e.clientX,clientY:e.clientY})),this._dragOrigin!==null){let s=ki(this._dragOrigin,t);this._editor.fire(\"selection:rectangle-update\",{rect:s});}this._updateNextAddCursor(e);}_handleClick(e){if(this._bondDragMoved){this._bondDragMoved=false;return}if(this._rectDragHappened){this._rectDragHappened=false;return}if(this._panMoved){this._panMoved=false;return}if(this._atomDragMoved){this._atomDragMoved=false;return}let t=this._toModel(e),n=this._tester.test(t),o=xi(e),r=this._editor.getMode();if(r===\"eraser\"){if(n?.atom!==void 0){this._editor.removeAtom(n.atom);return}if(n?.bond!==void 0){this._editor.removeBond(n.bond);return}return}if(n?.atom!==void 0){if(r===\"select\"&&!o.ctrl&&!o.shift&&!o.meta){let s=this._editor.getNextAddSymbol();if(s!==null){if(n.atom.biotype===s.biotype){this._editor.replaceMonomer(n.atom,s.symbol);return}this._editor.fire(\"editor:status\",{message:`Cannot replace: ${n.atom.biotype} is incompatible with 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0&&this._editor.fire(\"bond:contextmenu\",{bond:n.bond,clientX:e.clientX,clientY:e.clientY,preventDefault:r});}_handleMouseDown(e){if(e.button!==0)return;let t=this._toModel(e),n=this._tester.test(t),o=this._editor.getMode(),r=e.ctrlKey===true||e.metaKey===true,s=e.shiftKey===true;if(n?.atom!==void 0){if(o===\"move\"||o===\"select\"&&r){let a=this._editor.getSelection(),d=a.atoms.has(n.atom.id)?Array.from(a.atoms):[n.atom.id],c=this._editor.getMol(),u=new Map;for(let m of d){let p=c.atoms.find(h=>h.id===m);p!==void 0&&u.set(m,{x:p.p.x,y:p.p.y});}this._atomDragState={atomIds:d,pointerDownModel:{x:t.x,y:t.y},initialPositions:u},this._atomDragMoved=false;return}this._bondStart=n.atom,this._bondDragMoved=false;return}if(n===null){if(o===\"move\"||o===\"select\"&&!s){let a=this._editor.getViewport();this._panStart={origin:this._toViewBox({clientX:e.clientX,clientY:e.clientY}),initialOffset:{x:a.offset.x,y:a.offset.y}},this._panMoved=false;return}o===\"select\"&&s&&(this._dragOrigin=t,this._editor.fire(\"selection:rectangle-start\",{origin:t}));}}_handleMouseUp(e){if(this._panStart!==null){this._panStart=null;return}if(this._atomDragState!==null){this._atomDragState=null;return}if(this._bondStart!==null){let a=this._bondStart,l=this._bondDragMoved;this._bondStart=null;let d=this._toModel(e),u=this._tester.test(d)?.atom;if(l&&u!==void 0&&u.id!==a.id){if(this._editor.fire(\"bond:preview-end\",{start:a}),this._editor.getMode()===\"hbond\"){try{this._editor.addHydrogenBond(a,u);}catch{this._editor.fire(\"bond:cancel\",{start:a});}return}let m=a.bio.chainId===u.bio.chainId&&wi(a,u,this._editor.getMol())?\"backbone\":\"cross-polymer\",p=_i(a,u,this._editor.getMol().bonds,m);if(p.mode===\"fail\"){this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"editor:status\",{message:p.reason,severity:\"error\",durationMs:3e3});return}if(p.mode===\"auto\"){try{this._editor.addBond(a,u,p.r1,p.r2,p.kind);}catch{this._editor.fire(\"bond:cancel\",{start:a});}return}this._openChooseR(a,u,m,p.freeR1,p.freeR2);return}if(l){let m=this._addsEnabled()?this._editor.getNextAddSymbol():null;if(m!==null){let p;try{p=this._editor.addAtom(d,m.biotype,m.symbol);}catch{this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"bond:preview-end\",{start:a});return}let h=this._editor.getMol().atoms.find(M=>M.id===a.id);if(h===void 0){this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"bond:preview-end\",{start:a});return}let f=h.bio.chainId===p.bio.chainId&&wi(h,p,this._editor.getMol())?\"backbone\":\"cross-polymer\",y=W(h,this._editor.getMol().bonds),w=W(p,this._editor.getMol().bonds);if(y.includes(2)&&w.includes(1)){try{this._editor.addBond(h,p,2,1,f);}catch{this._editor.fire(\"bond:cancel\",{start:a});}this._editor.fire(\"bond:preview-end\",{start:a});return}let _=_i(h,p,this._editor.getMol().bonds,f);if(_.mode===\"fail\"){this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"editor:status\",{message:_.reason,severity:\"error\",durationMs:3e3}),this._editor.fire(\"bond:preview-end\",{start:a});return}if(_.mode===\"auto\"){try{this._editor.addBond(h,p,_.r1,_.r2,_.kind);}catch{this._editor.fire(\"bond:cancel\",{start:a});}this._editor.fire(\"bond:preview-end\",{start:a});return}this._editor.fire(\"bond:preview-end\",{start:a}),this._openChooseR(h,p,f,_.freeR1,_.freeR2);return}this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"bond:preview-end\",{start:a});return}return}if(this._dragOrigin===null)return;let t=this._toModel(e),n=ki(this._dragOrigin,t);this._dragOrigin=null;let o=this._tester.testRect(n),r=G.fromAtomsAndBonds(o.atoms.map(a=>a.id),o.bonds.map(a=>a.id)),s=G.union(this._editor.getSelection(),r);this._editor.setSelection(s),this._editor.fire(\"selection:rectangle-end\",{rect:n,selection:s}),this._rectDragHappened=true,s.atoms.size>0&&this._editor.getMode()===\"select\"&&this._editor.setMode(\"move\");}_handleMouseLeave(e){this._hoverAtom!==null&&(this._editor.fire(\"monomer:hover-end\",{atom:this._hoverAtom}),this._hoverAtom=null),this._hoverBond!==null&&(this._editor.fire(\"bond:hover-end\",{bond:this._hoverBond}),this._hoverBond=null),this._bondStart!==null&&(this._editor.fire(\"bond:cancel\",{start:this._bondStart}),this._editor.fire(\"bond:preview-end\",{start:this._bondStart}),this._bondStart=null,this._bondDragMoved=false),this._dragOrigin=null,this._panStart=null,this._atomDragState=null,this._panMoved=false,this._atomDragMoved=false,it(this._nextAddCursorEl);}_openChooseR(e,t,n,o,r){this._chooseRDialog===null&&(this._chooseRDialog=new Ve(this._editor)),this._chooseRDialog.open(e,t,{freeR1:o,freeR2:r}).then(a=>{if(!this._destroyed){if(a===null){this._editor.fire(\"bond:cancel\",{start:e});return}try{this._editor.addBond(e,t,a.r1,a.r2,n);}catch{this._editor.fire(\"bond:cancel\",{start:e});}}});}_updateNextAddCursor(e){let t=this._editor.getNextAddSymbol(),n=this._editor.getMode(),o=this._hoverAtom!==null,r=this._bondStart!==null||this._dragOrigin!==null||this._panStart!==null||this._atomDragState!==null;if(!(n===\"select\"&&t!==null&&!o&&!r)){this._nextAddCursorEl!==null&&it(this._nextAddCursorEl);return}let a=this._host.ownerDocument;if(a===null)return;this._nextAddCursorEl===null&&(this._nextAddCursorEl=yi(a));let l=this._editor.getService().monomerLib,d=null;for(let c of l.getPolymerTypes()){let u=l.getMonomer(c,t.symbol);if(u!==null){d=u;break}}gi(this._nextAddCursorEl,t.symbol,t.biotype,d,this._editor._currentTheme(),e.clientX,e.clientY);}_addsEnabled(){return this._editor.getMode()===\"select\"}_handleWheel(e){let t=e.ctrlKey===true||e.metaKey===true;if(e.preventDefault(),t){this._wheelPan(e);return}let n=e.deltaY<0?1.1:1/1.1,o=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),r=this._editor.getViewport(),s=r.scale===0?o:{x:(o.x-r.offset.x)/r.scale,y:(o.y-r.offset.y)/r.scale};this._editor.zoom(n,s);}_wheelPan(e){let t=e.deltaX??0,n=e.deltaY??0;if(t===0&&n===0)return;let o=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),r=this._toViewBox({clientX:e.clientX+t,clientY:e.clientY+n}),s=r.x-o.x,a=r.y-o.y,l=this._editor.getViewport();this._editor.panTo({x:l.offset.x-s,y:l.offset.y-a});}_toModel(e){let t=this._host.querySelector(\"svg\"),n=t!==null?t.querySelector(\".hw-content\"):null;if(t!==null&&n!==null){let r=vi(n,e.clientX,e.clientY);if(r!==null)return r;let s=this._host.getBoundingClientRect(),a=e.clientX-s.left,l=e.clientY-s.top,d=ta(n.getAttribute(\"transform\")??\"\");return d!==null?{x:(a-d.tx)/(d.scale===0?1:d.scale),y:(l-d.ty)/(d.scale===0?1:d.scale)}:{x:a,y:l}}let o=this._host.getBoundingClientRect();return {x:e.clientX-o.left,y:e.clientY-o.top}}_toViewBox(e){let t=this._host.querySelector(\"svg\");if(t!==null){let o=vi(t,e.clientX,e.clientY);if(o!==null)return o;let r=this._host.getBoundingClientRect(),s=e.clientX-r.left,a=e.clientY-r.top,l=ea(t.getAttribute(\"viewBox\"));return l!==null&&r.width>0&&r.height>0?{x:s*(l.w/r.width),y:a*(l.h/r.height)}:{x:s,y:a}}let n=this._host.getBoundingClientRect();return {x:e.clientX-n.left,y:e.clientY-n.top}}};function _i(i,e,t,n){let o=be(i),r=be(e);if(o===0||r===0)return {mode:\"auto\",r1:2,r2:1,kind:n};let s=W(i,t),a=W(e,t);if(s.length===0)return {mode:\"fail\",reason:`${i.symbol} has no free R-groups (max ${o}).`};if(a.length===0)return {mode:\"fail\",reason:`${e.symbol} has no free R-groups (max ${r}).`};if(s.includes(2)&&a.includes(1)&&(s.length===1||a.length===1))return 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a=r[1],l=(r[2]??\"\").split(/[,\\s]+/).map(d=>Number(d)).filter(d=>Number.isFinite(d));if(a===\"translate\"){let d=l[0]??0,c=l[1]??0;e=e+n*d,t=t+n*c;}else if(a===\"scale\"){let d=l[0]??1;n=n*d;}}return s?{tx:e,ty:t,scale:n}:null}function wi(i,e,t){if(i.bio.chainId!==e.bio.chainId)return  false;let n=t.chains.find(s=>s.id===i.bio.chainId);if(n===void 0)return  false;let o=-1,r=-1;for(let s=0;s<n.backboneAtoms.length;s++){let a=n.backboneAtoms[s];a.id===i.id&&(o=s),a.id===e.id&&(r=s);}return o<0||r<0?false:Math.abs(o-r)===1}function xi(i){return {shift:i.shiftKey===true,alt:i.altKey===true,ctrl:i.ctrlKey===true,meta:i.metaKey===true}}function ki(i,e){let t=Math.min(i.x,e.x),n=Math.min(i.y,e.y);return {x:t,y:n,width:Math.abs(i.x-e.x),height:Math.abs(i.y-e.y)}}var Ut=class{constructor(e,t,n){this._destroyed=false;this._host=e,this._editor=t,this._enabled=n?.enableKeyboard!==false,this._enabled&&e.getAttribute(\"tabindex\")===null&&e.setAttribute(\"tabindex\",\"0\"),this._onKey=o=>this._handleKey(o),e.addEventListener(\"keydown\",this._onKey);}destroy(){this._destroyed||(this._destroyed=true,this._host.removeEventListener(\"keydown\",this._onKey));}_handleKey(e){if(!this._enabled)return;let t=this._classify(e),n=na(e);if(t===null){this._editor.fire(\"key:unhandled\",{key:e.key,modifiers:n,preventDefault:()=>e.preventDefault()});return}let o=false,r=()=>{o=true,e.preventDefault();};this._editor.fire(\"key:command\",{command:t,preventDefault:r}),!o&&(e.preventDefault(),t!==\"clearSelection\"&&(e.stopPropagation(),e.stopImmediatePropagation?.()),this._execute(t));}_classify(e){let t=e.key,n=e.ctrlKey||e.metaKey;return t===\"Delete\"||t===\"Backspace\"?\"delete\":n&&(t===\"z\"||t===\"Z\")&&!e.shiftKey?\"undo\":n&&((t===\"z\"||t===\"Z\")&&e.shiftKey||t===\"y\"||t===\"Y\")?\"redo\":n&&(t===\"a\"||t===\"A\")?\"selectAll\":n&&(t===\"c\"||t===\"C\")?\"copy\":n&&(t===\"v\"||t===\"V\")?\"paste\":n&&(t===\"x\"||t===\"X\")?\"cut\":t===\"Escape\"?\"clearSelection\":t===\"+\"||t===\"=\"?\"zoomIn\":t===\"-\"||t===\"_\"?\"zoomOut\":t===\"0\"?\"fitToContent\":t===\"ArrowUp\"?\"nudgeUp\":t===\"ArrowDown\"?\"nudgeDown\":t===\"ArrowLeft\"?\"nudgeLeft\":t===\"ArrowRight\"?\"nudgeRight\":null}_execute(e){switch(e){case \"delete\":this._editor.deleteSelection();return;case \"undo\":this._editor.undo();return;case \"redo\":this._editor.redo();return;case \"selectAll\":this._editor.selectAll();return;case \"clearSelection\":this._editor.clearSelection();return;case \"zoomIn\":this._editor.zoom(1.1);return;case \"zoomOut\":this._editor.zoom(1/1.1);return;case \"fitToContent\":this._editor.fitToContent();return;case 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q(t.getMol(),t._currentTheme()),this._unsubs.push(t.on(\"mol:changed\",()=>{this._tester=new q(this._editor.getMol(),this._editor._currentTheme());})),this._onDragOver=n=>this._handleDragOver(n),this._onDrop=n=>this._handleDrop(n),this._onDragStart=n=>this._handleDragStart(n),this._onDragEnd=n=>this._handleDragEnd(n),this._onDragEnter=n=>this._handleDragEnter(n),this._onDragLeave=n=>this._handleDragLeave(n),e.addEventListener(\"dragover\",this._onDragOver),e.addEventListener(\"drop\",this._onDrop),e.addEventListener(\"dragstart\",this._onDragStart),e.addEventListener(\"dragend\",this._onDragEnd),e.addEventListener(\"dragenter\",this._onDragEnter),e.addEventListener(\"dragleave\",this._onDragLeave);}startPaletteDrag(e,t){this._currentPaletteSymbol=e,this._currentPaletteBiotype=t,this._editor.fire(\"dnd:start\",{source:\"palette\",symbol:e});}cancelPaletteDrag(){this._currentPaletteSymbol!==null&&(this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._editor.fire(\"dnd:cancel\",{source:\"palette\"}));}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this._host.removeEventListener(\"dragover\",this._onDragOver),this._host.removeEventListener(\"drop\",this._onDrop),this._host.removeEventListener(\"dragstart\",this._onDragStart),this._host.removeEventListener(\"dragend\",this._onDragEnd),this._host.removeEventListener(\"dragenter\",this._onDragEnter),this._host.removeEventListener(\"dragleave\",this._onDragLeave);}}_activePaletteSymbol(e){if(this._currentPaletteSymbol!==null&&this._currentPaletteBiotype!==null)return {symbol:this._currentPaletteSymbol,biotype:this._currentPaletteBiotype};let t=e.dataTransfer;if(t==null)return null;try{let n=typeof t.getData==\"function\"?t.getData(oa):\"\";if(n===\"\")return null;let o=JSON.parse(n);return typeof o.symbol!=\"string\"||typeof o.biotype!=\"string\"?null:{symbol:o.symbol,biotype:o.biotype}}catch{return null}}_handleDragEnter(e){if(this._activePaletteSymbol(e)!==null&&(e.preventDefault(),e.dataTransfer!==null&&e.dataTransfer!==void 0))try{e.dataTransfer.dropEffect=\"copy\";}catch{}}_handleDragLeave(e){}_handleDragOver(e){if(this._activePaletteSymbol(e)===null)return;if(e.preventDefault(),e.dataTransfer!==null&&e.dataTransfer!==void 0)try{e.dataTransfer.dropEffect=\"copy\";}catch{}let n=this._toModel(e),o=this._tester.test(n),r=o?.atom!==void 0?o.atom:o?.bond!==void 0?o.bond:void 0,s={clientX:e.clientX,clientY:e.clientY};r!==void 0&&(s.target=r),this._editor.fire(\"dnd:over\",s);}_handleDrop(e){let t=this._activePaletteSymbol(e);if(t===null)return;e.preventDefault();let{symbol:n,biotype:o}=t,r=this._toModel(e),s=this._tester.test(r),a=s?.atom!==void 0?s.atom:s?.bond!==void 0?s.bond:void 0,l={symbol:n,biotype:o,clientX:e.clientX,clientY:e.clientY};a!==void 0&&(l.target=a),this._editor.fire(\"dnd:drop\",l),s?.atom!==void 0?this._editor.replaceMonomer(s.atom,n):this._editor.addAtom(r,o,n),this._currentPaletteSymbol=null,this._currentPaletteBiotype=null;}_handleDragStart(e){this._editor.fire(\"dnd:start\",{source:\"canvas\"});}_handleDragEnd(e){this._currentPaletteSymbol!==null&&(this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._editor.fire(\"dnd:cancel\",{source:\"palette\"}));}_toModel(e){let t=this._host.querySelector(\"svg\"),n=t!==null?t.querySelector(\".hw-content\"):null;if(t!==null&&n!==null){let r=ia(n,e.clientX,e.clientY);if(r!==null)return r;let s=this._host.getBoundingClientRect(),a=e.clientX-s.left,l=e.clientY-s.top,d=ra(n.getAttribute(\"transform\")??\"\");return d!==null?{x:(a-d.tx)/(d.scale===0?1:d.scale),y:(l-d.ty)/(d.scale===0?1:d.scale)}:{x:a,y:l}}let o=this._host.getBoundingClientRect();return {x:e.clientX-o.left,y:e.clientY-o.top}}};function ia(i,e,t){let n=i;if(typeof n.getScreenCTM!=\"function\")return null;let o=n.getScreenCTM();if(o===null)return null;let r=null;try{let l=o;typeof l.inverse==\"function\"&&(r=l.inverse());}catch{return null}if(r===null)return null;let s=n.ownerSVGElement;if(s!=null&&typeof s.createSVGPoint==\"function\"){let l=s.createSVGPoint();l.x=e,l.y=t;let d=l.matrixTransform(r);return {x:d.x,y:d.y}}let a=r;return {x:a.a*e+a.c*t+a.e,y:a.b*e+a.d*t+a.f}}function ra(i){if(i===\"\")return null;let e=0,t=0,n=1,o=/(translate|scale)\\(([^)]+)\\)/g,r,s=false;for(;(r=o.exec(i))!==null;){s=true;let a=r[1],l=(r[2]??\"\").split(/[,\\s]+/).map(d=>Number(d)).filter(d=>Number.isFinite(d));if(a===\"translate\"){let d=l[0]??0,c=l[1]??0;e=e+n*d,t=t+n*c;}else if(a===\"scale\"){let d=l[0]??1;n=n*d;}}return s?{tx:e,ty:t,scale:n}:null}var Ue=class{constructor(e,t){this._modal=null;this._atom=null;this._editor=e;let n=e._getHost();if(n===null)throw new Error(\"AtomPropsDialog: editor has no host element.\");this._doc=t?.documentImpl??S(n);}get isOpen(){return this._modal!==null&&this._modal.isOpen}open(e){this.close(),this._atom=e;let t=this._editor._getHost();if(t===null)return;let n=new X(t,{documentImpl:this._doc,title:\"Monomer Properties\",testId:\"atom-props\"});this._modal=n;let o=g(this._doc,\"div\",{class:\"hw-modal__info\"},[`Position ${e.bio.continuousId} in ${e.bio.chainId}`]),r=Ne(this._doc,\"Symbol\",e.symbol,\"atom-props-symbol\"),s=Ne(this._doc,\"Annotation\",e.bio.annotation??\"\",\"atom-props-annotation\"),a=Ge(this._doc,\"atom-props\"),l=()=>this._commit(r.input.value,s.input.value);a.ok.addEventListener(\"click\",l),a.cancel.addEventListener(\"click\",()=>this.close()),n.setPrimaryAction(l),n.body.appendChild(o),n.body.appendChild(r.row),n.body.appendChild(s.row),n.body.appendChild(a.row),n.open();}close(){this._modal!==null&&(this._modal.close(),this._modal=null),this._atom=null;}_commit(e,t){let n=this._atom;if(n===null){this.close();return}let o=e.trim(),r=(n.bio.annotation??\"\")!==t;if(o.length>0&&o!==n.symbol&&this._editor.replaceMonomer(n,o),r){let a=new O(this._editor.getMol()),l={};l.tag=t===\"\"?void 0:t,a.updateAtom(n.id,l);let{mol:d}=a.commit();this._editor.setMol(d);let c=d.atoms.find(u=>u.id===n.id);if(c!==void 0){let u={atom:c};n.bio.annotation!==void 0&&(u.oldAnnotation=n.bio.annotation),t!==\"\"&&(u.newAnnotation=t),this._editor.fire(\"monomer:annotate\",u);}}this.close();}};var ze=class{constructor(e,t){this._modal=null;this._bond=null;this._editor=e;let n=e._getHost();if(n===null)throw new Error(\"BondPropsDialog: editor has no host element.\");this._doc=t?.documentImpl??S(n);}get isOpen(){return this._modal!==null&&this._modal.isOpen}open(e){this.close(),this._bond=e;let t=this._editor._getHost();if(t===null)return;let n=new X(t,{documentImpl:this._doc,title:\"Bond Properties\",testId:\"bond-props\"});this._modal=n;let o=g(this._doc,\"div\",{class:\"hw-modal__info\"},[`Kind: ${e.kind}`]),r=this._buildAtomsPreviewRow(e),s=e.r1.kind===\"numeric\",a=e.r2.kind===\"numeric\",l=s&&a,c=this._editor.getMol().bonds,u=l?Ai(e.r1,e.a1,c):[],m=l?Ai(e.r2,e.a2,c):[],p=null,h=null;if(l){let w=String(e.r1.r),_=String(e.r2.r);p=Fe(this._doc,`R-group on ${e.a1.symbol} (${e.a1.bio.chainId}:${e.a1.bio.positionInChain})`,u,w,\"bond-props-r1\"),h=Fe(this._doc,`R-group on ${e.a2.symbol} (${e.a2.bio.chainId}:${e.a2.bio.positionInChain})`,m,_,\"bond-props-r2\");}let f=Ge(this._doc,\"bond-props\"),y=()=>{let w=p!==null?Number(Mi(p.select,e.r1.r)):null,_=h!==null?Number(Mi(h.select,e.r2.r)):null;this._commit(w,_);};f.ok.addEventListener(\"click\",y),f.cancel.addEventListener(\"click\",()=>this.close()),n.setPrimaryAction(y),n.body.appendChild(o),r!==null&&n.body.appendChild(r),p!==null&&n.body.appendChild(p.row),h!==null&&n.body.appendChild(h.row),n.body.appendChild(f.row),n.open();}_buildAtomsPreviewRow(e){let t=this._rdkit(),n=this._buildAtomCell(e.a1,t,\"bond-props-atom-a1\"),o=this._buildAtomCell(e.a2,t,\"bond-props-atom-a2\"),r=g(this._doc,\"div\",{class:\"hw-bond-props__bond-arrow\"},[\"\\u2194\"]);return g(this._doc,\"div\",{class:\"hw-bond-props__atoms\",\"data-testid\":\"bond-props-atoms\"},[n,r,o])}_buildAtomCell(e,t,n){let o=e.monomer?.name??e.symbol,r=e.symbol===o?e.symbol:`${e.symbol} \\u2014 ${o}`,s=g(this._doc,\"div\",{class:\"hw-bond-props__atom-label\"},[r]),a={class:\"hw-bond-props__atom-rdkit\",\"data-testid\":`${n}-rdkit`},l=g(this._doc,\"div\",a),d=e.monomer?.smiles;if(t!==null&&d!==void 0&&d!==\"\"){let c=ye(t,d,220,140);c!==null&&c!==\"\"&&(l.innerHTML=c);}return g(this._doc,\"div\",{class:\"hw-bond-props__atom\",\"data-testid\":n},[s,l])}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}close(){this._modal!==null&&(this._modal.close(),this._modal=null),this._bond=null;}_commit(e,t){let n=this._bond;if(n===null){this.close();return}let o=n.r1.kind===\"numeric\"?n.r1.r:null,r=n.r2.kind===\"numeric\"?n.r2.r:null;if(!(e!==null&&t!==null&&(e!==o||t!==r))){this.close();return}if(e!==null&&t!==null){let a=n.kind,l=n.a1,d=n.a2;this._editor.removeBond(n);try{this._editor.addBond(l,d,e,t,a);}catch(c){if(o!==null&&r!==null)try{this._editor.addBond(l,d,o,r,n.kind);}catch{}}}this.close();}};function Ai(i,e,t){let n=e.monomer?.rgroups;if(n===void 0||n.length===0)return [{value:\"1\",label:\"R1\"},{value:\"2\",label:\"R2\"},{value:\"3\",label:\"R3\"}];let o=new Set(W(e,t));o.add(i.r);let r=Array.from(o).sort((a,l)=>a-l),s=[];for(let a of r){let l=n[a-1];if(l===void 0)continue;let d=l.capGroupName!==void 0&&l.capGroupName!==\"\"?` (${l.capGroupName})`:\"\";s.push({value:String(a),label:`${l.label}${d}`});}return s}function Mi(i,e){let t=i.value;if(typeof t==\"string\"&&t.length>0){let o=Number(t);if(Number.isFinite(o)&&o>=1)return o}let n=i.querySelectorAll(\"option\");for(let o of Array.from(n))if(o.getAttribute(\"selected\")!==null){let r=o.getAttribute(\"value\")??\"\",s=Number(r);if(Number.isFinite(s)&&s>=1)return s}return e}var Ke=class{constructor(e,t){this._modal=null;this._result=null;this._findInput=null;this._replaceInput=null;this._matches=[];this._cursor=-1;this._editor=e;let n=e._getHost();if(n===null)throw new Error(\"FindReplaceDialog: editor has no host element.\");this._doc=t?.documentImpl??S(n);}get isOpen(){return this._modal!==null&&this._modal.isOpen}open(){this.close();let e=this._editor._getHost();if(e===null)return;let t=new X(e,{documentImpl:this._doc,title:\"Find / Replace\",testId:\"find-replace\"});this._modal=t;let n=Ne(this._doc,\"Find\",\"\",\"find-replace-find\"),o=Ne(this._doc,\"Replace with\",\"\",\"find-replace-replace\");this._findInput=n.input,this._replaceInput=o.input;let r=this._doc.createElement(\"button\");r.setAttribute(\"class\",\"hw-modal__find-next\"),r.setAttribute(\"type\",\"button\"),r.setAttribute(\"data-testid\",\"find-replace-next\"),r.appendChild(this._doc.createTextNode(\"Find Next\")),r.addEventListener(\"click\",()=>this._findNext());let s=this._doc.createElement(\"button\");s.setAttribute(\"class\",\"hw-modal__replace\"),s.setAttribute(\"type\",\"button\"),s.setAttribute(\"data-testid\",\"find-replace-replace-one\"),s.appendChild(this._doc.createTextNode(\"Replace\")),s.addEventListener(\"click\",()=>this._replaceOne());let a=this._doc.createElement(\"button\");a.setAttribute(\"class\",\"hw-modal__replace-all\"),a.setAttribute(\"type\",\"button\"),a.setAttribute(\"data-testid\",\"find-replace-replace-all\"),a.appendChild(this._doc.createTextNode(\"Replace All\")),a.addEventListener(\"click\",()=>this._replaceAll());let l=this._doc.createElement(\"button\");l.setAttribute(\"class\",\"hw-modal__cancel\"),l.setAttribute(\"type\",\"button\"),l.setAttribute(\"data-testid\",\"find-replace-close\"),l.appendChild(this._doc.createTextNode(\"Close\")),l.addEventListener(\"click\",()=>this.close());let d=g(this._doc,\"div\",{class:\"hw-modal__actions\"},[r,s,a,l]),c=g(this._doc,\"div\",{class:\"hw-modal__result\",\"data-testid\":\"find-replace-result\"},[\"0 matches\"]);this._result=c,t.setPrimaryAction(()=>this._findNext()),t.body.appendChild(n.row),t.body.appendChild(o.row),t.body.appendChild(d),t.body.appendChild(c),t.open();}close(){this._modal!==null&&(this._modal.close(),this._modal=null),this._result=null,this._findInput=null,this._replaceInput=null,this._matches=[],this._cursor=-1;}_findNext(){let e=this._findInput?.value.trim()??\"\";if(e===\"\"){this._setResultText(\"Enter a symbol to find\");return}let t=this._editor.findMonomers(e);if(this._matches=t.map(o=>o.id),this._matches.length===0){this._cursor=-1,this._editor.setHighlights([]),this._setResultText(\"No matches\");return}this._cursor=(this._cursor+1)%this._matches.length;let n=this._matches[this._cursor];n!==void 0&&this._editor.setHighlights([n]),this._setResultText(`${this._cursor+1} / ${this._matches.length} matches`);}_replaceOne(){let e=this._findInput?.value.trim()??\"\",t=this._replaceInput?.value.trim()??\"\";if(e===\"\"||t===\"\"){this._setResultText(\"Both Find and Replace fields are required\");return}if(this._matches.length===0||this._cursor<0){this._findNext();return}let n=this._matches[this._cursor];if(n===void 0)return;let o=this._editor.getMol().atoms.find(r=>r.id===n);if(o!==void 0)if(this._editor.replaceMonomer(o,t),this._matches.splice(this._cursor,1),this._matches.length===0)this._cursor=-1,this._editor.setHighlights([]),this._setResultText(\"Replaced; no further matches\");else {this._cursor=this._cursor%this._matches.length;let r=this._matches[this._cursor];r!==void 0&&this._editor.setHighlights([r]),this._setResultText(`${this._matches.length} matches remaining`);}}_replaceAll(){let e=this._findInput?.value.trim()??\"\",t=this._replaceInput?.value.trim()??\"\";if(e===\"\"||t===\"\"){this._setResultText(\"Both Find and Replace fields are required\");return}let n=this._editor.replaceMonomers(e,t);this._matches=[],this._cursor=-1,this._editor.setHighlights([]),this._setResultText(`${n} replacement${n===1?\"\":\"s\"} made`);}_setResultText(e){if(this._result!==null){for(;this._result.firstChild!==null;)this._result.removeChild(this._result.firstChild);this._result.appendChild(this._doc.createTextNode(e));}}};var ge=Object.freeze(new Set),sa=.2,aa=8,rt=class{constructor(e,t){this._events=new De;this._destroyed=false;this._view=null;this._pointer=null;this._keyboard=null;this._dnd=null;this._atomDialog=null;this._bondDialog=null;this._findReplaceDialog=null;this._viewBootstrapped=false;this._mode=\"select\";this._nextAdd=null;this._lastAction=null;this._lastTripletSugarPos=null;if(t.service===void 0||t.service===null)throw new TypeError(\"HelmEditor: options.service is required\");this._host=e,this._service=t.service,this._options=Object.freeze({...t}),this._mol=me(),this._selection=G.empty(),this._highlights=ge,this._theme=t.service.theme??H,this._viewport={scale:1,offset:{x:0,y:0}},this._viewOnly=t.viewOnly??false,this._history=new Oe({maxEntries:100}),this._history.push({mol:this._mol,label:\"initial\"}),this._libUnsub=this._service.monomerLib.onChanged.subscribe(n=>{let o=this._service.monomerLib,r=typeof o.version==\"number\"?o.version:0,s=n.type===\"reload\"?\"replace\":\"update\";this._events.fire(\"monomer-lib:change\",{source:this._service.monomerLib.source,version:r,reason:s});}),t.initialHelm!==void 0&&this.setHelm(t.initialHelm),this._bootstrapWaveB();}_bootstrapWaveB(){if(this._viewBootstrapped||this._host===null)return;let e=this._resolveDocument(this._host);if(e===null)return;this._viewBootstrapped=true;let t={documentImpl:e};this._options.width!==void 0&&(t.width=this._options.width),this._options.height!==void 0&&(t.height=this._options.height),this._view=new Nt(this._host,this,t),this._viewOnly!==true&&(this._pointer=new Vt(this._host,this,{enableContextMenu:this._options.enableContextMenu??true})),this._options.enableKeyboard!==false&&(this._keyboard=new Ut(this._host,this,{enableKeyboard:true})),this._options.enableDragDrop!==false&&(this._dnd=new zt(this._host,this)),this._events.on(\"monomer:hover\",n=>{this.setHighlights([n.atom.id]);}),this._events.on(\"monomer:hover-end\",()=>{this.clearHighlights();}),this._events.on(\"monomer:click\",n=>{let o=n.modifiers;if(o.ctrl===true||o.meta===true){this.setSelection(G.toggle(this._selection,{kind:\"atom\",id:n.atom.id}));return}if(o.shift===true){this.setSelection(G.union(this._selection,G.fromAtoms([n.atom.id])));return}this.setSelection(G.fromAtoms([n.atom.id]));});}_resolveDocument(e){let t=e.ownerDocument;if(t!=null)return t;let n=globalThis;return n.document!==void 0?n.document:null}destroy(){this._destroyed||(this._destroyed=true,this._atomDialog!==null&&(this._atomDialog.close(),this._atomDialog=null),this._bondDialog!==null&&(this._bondDialog.close(),this._bondDialog=null),this._findReplaceDialog!==null&&(this._findReplaceDialog.close(),this._findReplaceDialog=null),this._dnd!==null&&(this._dnd.destroy(),this._dnd=null),this._keyboard!==null&&(this._keyboard.destroy(),this._keyboard=null),this._pointer!==null&&(this._pointer.destroy(),this._pointer=null),this._view!==null&&(this._view.destroy(),this._view=null),this._libUnsub(),this._events.clear(),this._history.clear());}resize(e,t){this._ensureLive(),this._view!==null&&this._view.resize(e,t),this._events.fire(\"view:resize\",{width:e,height:t});}redraw(){if(this._ensureLive(),this._view!==null){this._view.redraw();return}this._events.fire(\"render:skip\",{reason:\"no-view-mounted\"});}setHelm(e,t){this._ensureLive();let n=t?.canonicalize??this._options.canonicalize??false,o=this._service.parse(e,{mode:\"lenient\"}),r=o.diagnostics;r.filter(d=>d.severity===\"error\").length>0&&this._events.fire(\"helm:parse-error\",{helm:e,diagnostics:r});for(let d of r)d.severity===\"error\"?this._events.fire(\"validation:error\",{diagnostic:d}):d.severity===\"warning\"&&this._events.fire(\"validation:warning\",{diagnostic:d});let a=o.mol;if(n){let d=this._service.canonicalize(e);a=this._service.parse(d,{mode:\"lenient\"}).mol;}let l=ne(a,this._options.bondLength!==void 0?{bondLength:this._options.bondLength}:void 0);return this._replaceMol(l,\"setHelm\",\"api\"),{mol:l,diagnostics:r}}getHelm(e){this._ensureLive();let t={};return e?.canonicalize!==void 0&&(t.canonicalize=e.canonicalize),e?.includeHighlights!==void 0&&(t.includeHighlights=e.includeHighlights),this._service.serialize(this._mol,t)}setMol(e){this._ensureLive(),this._replaceMol(e,\"setMol\",\"api\");}getMol(){return this._mol}getService(){return this._service}getSelection(){return this._selection}setSelection(e){if(this._ensureLive(),G.equals(this._selection,e))return;let t=G.difference(e,this._selection),n=G.difference(this._selection,e);this._selection=e,this._events.fire(\"selection:change\",{selection:e,addedAtomIds:t.atoms,removedAtomIds:n.atoms,addedBondIds:t.bonds,removedBondIds:n.bonds});}selectAll(){this._ensureLive();let e=this._mol.atoms.map(n=>n.id),t=this._mol.bonds.map(n=>n.id);this.setSelection(G.fromAtomsAndBonds(e,t));}clearSelection(){this._ensureLive(),!this._selection.isEmpty&&this.setSelection(G.empty());}setHighlights(e){this._ensureLive();let t=new Set(e);this._highlights=t,this._events.fire(\"highlight:change\",{atomIds:t,bondIds:ge});}clearHighlights(){this._ensureLive(),this._highlights.size!==0&&(this._highlights=ge,this._events.fire(\"highlight:change\",{atomIds:ge,bondIds:ge}));}addAtom(e,t,n){this._ensureLive();let o=new O(this._mol),r=o.addAtom({p:e,biotype:t,symbol:n}),{mol:s}=o.commit(),a=xe(s,this._service.monomerLib,{mode:\"lenient\"}).mol;this._replaceMol(a,`addAtom:${n}`,\"api\");let l=J(a,r);if(l===void 0)throw new Error(\"HelmEditor.addAtom: lost atom after commit\");return this._events.fire(\"monomer:add\",{atom:l,source:\"api\"}),l}removeAtom(e){this._ensureLive();let t=typeof e==\"number\"?e:e.id,n=J(this._mol,t);if(n===void 0)return;let o=new O(this._mol);o.removeAtom(t);let{mol:r}=o.commit();this._replaceMol(r,`removeAtom:${n.symbol}`,\"api\"),this._events.fire(\"monomer:remove\",{atom:n,source:\"api\"});}addBond(e,t,n,o,r){this._ensureLive();let s,a;try{this._validateAddBondConstraints(e,t,n,o);let d=r??\"backbone\",c=this._maybeMergeForLinearExtend(e,t,n,o,d);if(c!==null)({id:s,mol:a}=c);else {let u=new O(this._mol);s=u.addBond({a1:e.id,a2:t.id,kind:r??\"backbone\",r1:{kind:\"numeric\",r:n},r2:{kind:\"numeric\",r:o}}),{mol:a}=u.commit();}}catch(d){let c=d instanceof I?d.message:this._friendlyBondError(d instanceof Error?d.message:String(d),e,t,n,o);throw this._events.fire(\"editor:status\",{message:`Could not add bond: ${c}`,severity:\"error\",durationMs:3e3}),d}this._replaceMol(a,\"addBond\",\"api\");let l=_t(a,s);if(l===void 0)throw new Error(\"HelmEditor.addBond: lost bond after commit\");return this._events.fire(\"bond:add\",{bond:l,source:\"api\"}),l}_maybeMergeForLinearExtend(e,t,n,o,r){if(e.bio.chainId===t.bio.chainId||r!==\"backbone\"&&r!==\"cross-polymer\")return null;let s=this._mol.chains.find(l=>l.id===e.bio.chainId),a=this._mol.chains.find(l=>l.id===t.bio.chainId);if(s===void 0||a===void 0||s.polymerType!==a.polymerType)return null;if(n===2&&o===1){let l=s.backboneAtoms[s.backboneAtoms.length-1],d=a.backboneAtoms[0];if(l!==void 0&&d!==void 0&&l.id===e.id&&d.id===t.id)return this._mergeChains(s,a,r)}if(n===1&&o===2){let l=s.backboneAtoms[0],d=a.backboneAtoms[a.backboneAtoms.length-1];if(l!==void 0&&d!==void 0&&l.id===e.id&&d.id===t.id)return this._mergeChains(a,s,r)}return null}_mergeChains(e,t,n){let o=e.backboneAtoms.length,r=new Set;for(let _ of t.backboneAtoms)r.add(_.id),_.branchAtom!==void 0&&r.add(_.branchAtom.id);let s=new Map,a=o;for(let _ of t.backboneAtoms){a+=1;let M={..._,bio:{..._.bio,chainId:e.id,positionInChain:a}};if(s.set(_.id,M),_.branchAtom!==void 0){let k=_.branchAtom,x={...k,bio:{...k.bio,chainId:e.id,positionInChain:a}};s.set(k.id,x);}}for(let _ of t.backboneAtoms){let M=s.get(_.id);if(M===void 0||_.branchAtom===void 0)continue;let k=s.get(_.branchAtom.id);k!==void 0&&(M.branchAtom=k);}for(let _ of this._mol.atoms)s.has(_.id)||s.set(_.id,_);let l=0;for(let _ of this._mol.atoms)_.id>l&&(l=_.id);for(let _ of this._mol.bonds)_.id>l&&(l=_.id);let d=l+1,c=s.get(e.backboneAtoms[e.backboneAtoms.length-1].id),u=s.get(t.backboneAtoms[0].id),m={id:d,a1:c,a2:u,kind:\"backbone\",r1:{kind:\"numeric\",r:2},r2:{kind:\"numeric\",r:1}},p=[];for(let _ of this._mol.bonds){let M=s.get(_.a1.id)??_.a1,k=s.get(_.a2.id)??_.a2;M===_.a1&&k===_.a2?p.push(_):p.push({..._,a1:M,a2:k});}p.push(m);let h=[],f=[...e.backboneAtoms];for(let _ of t.backboneAtoms)f.push(s.get(_.id));for(let _ of this._mol.chains)if(_.id!==t.id)if(_.id===e.id){let M=_.bonds.map(k=>{let x=s.get(k.a1.id)??k.a1,T=s.get(k.a2.id)??k.a2;return x===k.a1&&T===k.a2?k:{...k,a1:x,a2:T}});for(let k of t.bonds){let x=s.get(k.a1.id)??k.a1,T=s.get(k.a2.id)??k.a2;M.push(x===k.a1&&T===k.a2?k:{...k,a1:x,a2:T});}M.push(m),h.push({id:_.id,polymerType:_.polymerType,backboneAtoms:f,bonds:M,..._.annotation!==void 0?{annotation:_.annotation}:{}});}else {let M=_.backboneAtoms.map(x=>s.get(x.id)??x),k=_.bonds.map(x=>{let T=s.get(x.a1.id)??x.a1,E=s.get(x.a2.id)??x.a2;return T===x.a1&&E===x.a2?x:{...x,a1:T,a2:E}});h.push({id:_.id,polymerType:_.polymerType,backboneAtoms:M,bonds:k,..._.annotation!==void 0?{annotation:_.annotation}:{}});}let w={atoms:this._mol.atoms.map(_=>s.get(_.id)??_),bonds:p,chains:h,groups:this._mol.groups,annotations:this._mol.annotations};return w=this._refreshContinuousIdsLocal(w),{id:d,mol:w}}_refreshContinuousIdsLocal(e){let t=Ee(e),n=new Map;for(let l of e.atoms){let d=t.get(l.id);if(d===void 0||d===l.bio.continuousId){n.set(l.id,l);continue}n.set(l.id,{...l,bio:{...l.bio,continuousId:d}});}for(let l of e.atoms){if(l.branchAtom===void 0)continue;let d=n.get(l.id),c=n.get(l.branchAtom.id);d===void 0||c===void 0||(d.branchAtom=c);}let o=e.bonds.map(l=>{let d=n.get(l.a1.id)??l.a1,c=n.get(l.a2.id)??l.a2;return d===l.a1&&c===l.a2?l:{...l,a1:d,a2:c}}),r=new Map;for(let l of o)r.set(l.id,l);let s=e.chains.map(l=>{let d=l.backboneAtoms.map(u=>n.get(u.id)??u),c=l.bonds.map(u=>r.get(u.id)??u);return {id:l.id,polymerType:l.polymerType,backboneAtoms:d,bonds:c,...l.annotation!==void 0?{annotation:l.annotation}:{}}});return {atoms:e.atoms.map(l=>n.get(l.id)??l),bonds:o,chains:s,groups:e.groups,annotations:e.annotations}}_friendlyBondError(e,t,n,o,r){return e.includes(\"duplicate bond\")?`bond ${t.symbol}:R${o} \\u2194 ${n.symbol}:R${r} already exists`:e.includes(\"does not exist\")?\"one of the endpoint atoms is missing\":e}_validateAddBondConstraints(e,t,n,o){let r=this._mol.bonds,s=be(e);if(s>0&&(n<1||n>s))throw new I(\"rgroup-not-on-monomer\",`R-group R${n} is not defined on monomer '${e.symbol}' (has R1..R${s})`,{atomId:e.id,requested:n,total:s});let a=be(t);if(a>0&&(o<1||o>a))throw new I(\"rgroup-not-on-monomer\",`R-group R${o} is not defined on monomer '${t.symbol}' (has R1..R${a})`,{atomId:t.id,requested:o,total:a});if(s>0){let l=Ht(e,r).find(d=>d.rNumber===n);if(l!==void 0){let d=l.side===\"r1\"?l.bond.a2:l.bond.a1;throw new I(\"rgroup-already-bonded\",`R-group R${n} on '${e.symbol}' is already bonded to '${d.symbol}' (${d.bio.chainId}:${d.bio.positionInChain})`,{atomId:e.id,requested:n,conflictingBondId:l.bond.id})}}if(a>0){let l=Ht(t,r).find(d=>d.rNumber===o);if(l!==void 0){let d=l.side===\"r1\"?l.bond.a2:l.bond.a1;throw new I(\"rgroup-already-bonded\",`R-group R${o} on '${t.symbol}' is already bonded to '${d.symbol}' (${d.bio.chainId}:${d.bio.positionInChain})`,{atomId:t.id,requested:o,conflictingBondId:l.bond.id})}}for(let l of r){if(l.r1.kind!==\"numeric\"||l.r2.kind!==\"numeric\")continue;let d=l.a1.id===e.id&&l.a2.id===t.id&&l.r1.r===n&&l.r2.r===o,c=l.a1.id===t.id&&l.a2.id===e.id&&l.r1.r===o&&l.r2.r===n;if(d||c)throw new I(\"duplicate-bond\",`bond ${e.symbol}:R${n} \\u2194 ${t.symbol}:R${o} already exists`,{atomId:e.id,bondId:l.id})}}_freeRgroupsOn(e){return W(e,this._mol.bonds)}addHydrogenBond(e,t){this._ensureLive();let n=new O(this._mol),o={kind:\"pair\"},r=n.addBond({a1:e.id,a2:t.id,kind:\"hbond\",r1:o,r2:o}),{mol:s}=n.commit();this._replaceMol(s,\"addHydrogenBond\",\"api\");let a=_t(s,r);if(a===void 0)throw new Error(\"HelmEditor.addHydrogenBond: lost bond after commit\");return this._events.fire(\"bond:add\",{bond:a,source:\"api\"}),a}removeBond(e){this._ensureLive();let t=typeof e==\"number\"?e:e.id,n=_t(this._mol,t);if(n===void 0)return;let o=new O(this._mol);o.removeBond(t);let{mol:r}=o.commit();this._replaceMol(r,\"removeBond\",\"api\"),this._events.fire(\"bond:remove\",{bond:n,source:\"api\"});}replaceMonomer(e,t){this._ensureLive();let n=J(this._mol,e.id);if(n===void 0)return;let o=n.symbol;if(o===t)return;let r=new O(this._mol);r.updateAtom(e.id,{symbol:t});let{mol:s}=r.commit(),a=xe(s,this._service.monomerLib,{mode:\"lenient\"}).mol;this._replaceMol(a,`replaceMonomer:${o}->${t}`,\"api\");let l=J(a,e.id);l!==void 0&&this._events.fire(\"monomer:replace\",{atom:l,oldSymbol:o,newSymbol:t});}hitTest(e,t){this._ensureLive();let o=new q(this._mol,this._theme).test({x:e,y:t});return o===null?null:o.atom!==void 0?{atom:o.atom}:o.bond!==void 0?{bond:o.bond}:null}moveAtom(e,t){this._ensureLive();let n=J(this._mol,e);if(n===void 0||n.p.x===t.x&&n.p.y===t.y)return;let o=new O(this._mol);o.updateAtom(e,{p:{x:t.x,y:t.y}});let{mol:r}=o.commit();this._replaceMol(r,\"moveAtom\",\"user\");}moveAtoms(e){if(this._ensureLive(),e.length===0)return;let t=new O(this._mol),n=0;for(let r of e){let s=J(this._mol,r.atomId);s!==void 0&&(s.p.x===r.p.x&&s.p.y===r.p.y||(t.updateAtom(r.atomId,{p:{x:r.p.x,y:r.p.y}}),n+=1));}if(n===0)return;let{mol:o}=t.commit();this._replaceMol(o,\"moveAtom\",\"user\");}cleanLayout(e){this._ensureLive(),this._resetLastAction();let t=ne(this._mol,this._options.bondLength!==void 0?{bondLength:this._options.bondLength}:void 0);this._mol=t,this._history.push({mol:t,label:\"cleanLayout\"}),this._events.fire(\"layout:change\",{mol:t,strategy:\"auto\"}),this._events.fire(\"mol:changed\",{mol:t,changedAtomIds:new Set(t.atoms.map(n=>n.id)),changedBondIds:ge,reason:\"cleanLayout\"});}canUndo(){return this._history.canUndo()}canRedo(){return this._history.canRedo()}undo(){this._ensureLive();let e=this._history.undo();e!==null&&this._restoreFromHistory(e.mol,\"undo\");}redo(){this._ensureLive();let e=this._history.redo();e!==null&&this._restoreFromHistory(e.mol,\"redo\");}on(e,t){return this._events.on(e,t)}off(e,t){this._events.off(e,t);}fire(e,t){this._events.fire(e,t);}zoom(e,t){if(this._ensureLive(),!Number.isFinite(e)||e<=0)return;let n=this._viewport.scale,o=Math.min(aa,Math.max(sa,n*e));if(o===n)return;let r={...this._viewport.offset},s=r;t!==void 0&&(s={x:r.x+(n-o)*t.x,y:r.y+(n-o)*t.y});let a={scale:o,offset:s};this._viewport=a;let l=t??{x:0,y:0};this._events.fire(\"view:zoom\",{scale:o,center:l,previousScale:n}),this._events.fire(\"view:viewport-change\",{viewport:a});}panTo(e){this._ensureLive();let t={...this._viewport.offset},n={scale:this._viewport.scale,offset:{...e}};this._viewport=n,this._events.fire(\"view:pan\",{offset:n.offset,previousOffset:t}),this._events.fire(\"view:viewport-change\",{viewport:n});}getViewport(){return {scale:this._viewport.scale,offset:{...this._viewport.offset}}}fitToContent(e){this._ensureLive();let t=0,n=0,o=0,r=0,s=false;for(let u of this._mol.atoms){if(!s){t=o=u.p.x,n=r=u.p.y,s=true;continue}u.p.x<t&&(t=u.p.x),u.p.x>o&&(o=u.p.x),u.p.y<n&&(n=u.p.y),u.p.y>r&&(r=u.p.y);}let a=s?{x:t,y:n,width:o-t,height:r-n}:{x:0,y:0,width:0,height:0},l={...this._viewport.offset},d=this._viewport.scale,c={scale:1,offset:{x:0,y:0}};this._viewport=c,d!==1&&this._events.fire(\"view:zoom\",{scale:1,center:{x:0,y:0},previousScale:d}),(l.x!==0||l.y!==0)&&this._events.fire(\"view:pan\",{offset:c.offset,previousOffset:l}),this._events.fire(\"view:viewport-change\",{viewport:c}),this._events.fire(\"view:fit-to-content\",{bbox:a});}setViewOnly(e){this._ensureLive();let t=this._viewOnly;t!==e&&(this._viewOnly=e,this._events.fire(\"option:change\",{key:\"viewOnly\",oldValue:t,newValue:e}));}setTheme(e){this._ensureLive();let t=this._theme;t!==e&&(this._theme=e,this._events.fire(\"theme:change\",{theme:e,previousTheme:t}));}toSvg(e){this._ensureLive();let t=this.getHelm(),n={};return e?.width!==void 0&&(n.width=e.width),e?.height!==void 0&&(n.height=e.height),this._service.renderToSvg(t,n)}async toPng(e){this._ensureLive();let t=this.getHelm(),n={};return e?.width!==void 0&&(n.width=e.width),e?.height!==void 0&&(n.height=e.height),this._service.renderToPng(t,n)}_getHost(){return this._host}_observerCount(){return this._events.observerCount()}_currentHighlights(){return this._highlights}_currentTheme(){return this._theme}_getView(){return this._view}_getViewport(){return this._viewport}openAtomProps(e){this._ensureLive(),this._host!==null&&(this._atomDialog===null&&(this._atomDialog=new Ue(this)),this._atomDialog.open(e));}openBondProps(e){this._ensureLive(),this._host!==null&&(this._bondDialog===null&&(this._bondDialog=new ze(this)),this._bondDialog.open(e));}openFindReplace(){this._ensureLive(),this._host!==null&&(this._findReplaceDialog===null&&(this._findReplaceDialog=new Ke(this)),this._findReplaceDialog.open());}getMode(){return this._mode}setMode(e){this._ensureLive();let t=this._mode;t!==e&&(this._mode=e,this._events.fire(\"option:change\",{key:\"mode\",oldValue:t,newValue:e}));}getNextAddSymbol(){return this._nextAdd}setNextAddSymbol(e,t){this._ensureLive();let n=this._nextAdd;if(e===null)this._nextAdd=null;else {if(t===void 0)return;this._nextAdd={symbol:e,biotype:t};}this._events.fire(\"option:change\",{key:\"nextAdd\",oldValue:n,newValue:this._nextAdd});}startPaletteDrag(e,t){if(this._ensureLive(),this._dnd===null){this._events.fire(\"dnd:start\",{source:\"palette\",symbol:e});return}this._dnd.startPaletteDrag(e,t);}findMonomers(e){this._ensureLive();let t=[];for(let n of this._mol.atoms)n.symbol===e&&t.push(n);return t}replaceMonomers(e,t){this._ensureLive();let n,o;if(typeof e==\"string\"){let d=e,c=t;if(n=this.findMonomers(d),n.length===0)return 0;if(d===c)return n.length;o=`${d}->${c}`;}else {let d=t,c=new Set,u=[];for(let m of e){if(c.has(m.id))continue;c.add(m.id);let p=J(this._mol,m.id);p!==void 0&&p.symbol!==d&&u.push(p);}if(u.length===0)return 0;n=u,o=`atoms[${u.length}]->${d}`;}let r=t,s=new O(this._mol);for(let d of n)s.updateAtom(d.id,{symbol:r});let{mol:a}=s.commit(),l=xe(a,this._service.monomerLib,{mode:\"lenient\"}).mol;return this._replaceMol(l,`replaceMonomers:${o}`,\"api\"),n.length}nudgeSelection(e,t){this._ensureLive();let n=this._selection;if(n.atoms.size===0)return;let o=new O(this._mol);for(let s of n.atoms){let a=J(this._mol,s);a!==void 0&&o.updateAtom(s,{p:{x:a.p.x+e,y:a.p.y+t}});}let{mol:r}=o.commit();this._replaceMol(r,\"nudge\",\"user\");}deleteSelection(){this._ensureLive();let e=this._selection;if(e.atoms.size===0&&e.bonds.size===0)return;let t=new O(this._mol);for(let o of e.atoms)t.removeAtom(o);for(let o of e.bonds)t.removeBond(o);let{mol:n}=t.commit();this._selection=G.empty(),this._replaceMol(n,\"delete-selection\",\"user\"),this._events.fire(\"selection:change\",{selection:this._selection,addedAtomIds:ge,removedAtomIds:e.atoms,addedBondIds:ge,removedBondIds:e.bonds});}appendRnaTriplet(e,t,n){this._ensureLive();let o=We(e,t,n),r=this.getHelm(),s=da(r,o);this.setHelm(s);}placeRnaTriplet(e,t,n){this._ensureLive();let o=1.6*(this._options.bondLength??28),r,s=this._mol.atoms;if(this._lastAction===\"add-triplet\"&&this._lastTripletSugarPos!==null)r={x:this._lastTripletSugarPos.x+o*2,y:this._lastTripletSugarPos.y};else if(s.length===0)r={x:0,y:0};else {let M=s[0].p.x,k=s[0].p.y;for(let x of s)x.p.x<M&&(M=x.p.x),x.p.y>k&&(k=x.p.y);r={x:M,y:k+o};}let a={x:r.x+o,y:r.y},l={x:r.x,y:r.y+o},d=new Set;for(let M of this._mol.chains)d.add(M.id);let c=1;for(;d.has(`RNA${c}`);)c+=1;let u=`RNA${c}`,m=new O(this._mol),p=m.addAtom({p:r,biotype:b.SUGAR,symbol:e,chainId:u,positionInChain:1}),h=m.addAtom({p:a,biotype:b.LINKER,symbol:n,chainId:u,positionInChain:2}),f=m.addAtom({p:l,biotype:b.BASE,symbol:t,chainId:u,positionInChain:0});m.addBond({a1:p,a2:f,kind:\"branch\",r1:{kind:\"numeric\",r:3},r2:{kind:\"numeric\",r:1}}),m.addBond({a1:p,a2:h,kind:\"backbone\",r1:{kind:\"numeric\",r:2},r2:{kind:\"numeric\",r:1}});let{mol:y}=m.commit(),w=this._postProcessTripletMol(y,p,f,u),_=xe(w,this._service.monomerLib,{mode:\"lenient\"}).mol;this._replaceMol(_,\"placeRnaTriplet\",\"user\"),this._lastAction=\"add-triplet\",this._lastTripletSugarPos=r;}_postProcessTripletMol(e,t,n,o){let r=new Map,s=J(e,n),a=J(e,t);if(s===void 0||a===void 0)return e;let l={...a,branchAtom:s};r.set(t,l);let d=e.bonds.map(h=>{let f=r.get(h.a1.id)??h.a1,y=r.get(h.a2.id)??h.a2;return f===h.a1&&y===h.a2?h:{...h,a1:f,a2:y}}),c=new Map;for(let h of d)c.set(h.id,h);let u=e.chains.map(h=>{let f=[];for(let w of h.backboneAtoms)h.id===o&&w.id===n||f.push(r.get(w.id)??w);let y=h.bonds.map(w=>c.get(w.id)??w);return {id:h.id,polymerType:h.polymerType,backboneAtoms:f,bonds:y,...h.annotation!==void 0?{annotation:h.annotation}:{}}}),p={atoms:e.atoms.map(h=>r.get(h.id)??h),bonds:d,chains:u,groups:e.groups,annotations:e.annotations};return p=this._refreshContinuousIdsLocal(p),p}_resetLastAction(){this._lastAction=\"other\",this._lastTripletSugarPos=null;}_ensureLive(){if(this._destroyed)throw new Error(\"HelmEditor: this instance has been destroyed.\")}_replaceMol(e,t,n){let o=this._service.serialize(this._mol),r=this._service.serialize(e);this._mol=e,this._history.push({mol:e,label:t}),this._resetLastAction(),this._events.fire(\"mol:changed\",{mol:e,changedAtomIds:new Set(e.atoms.map(s=>s.id)),changedBondIds:new Set(e.bonds.map(s=>s.id)),reason:t}),o!==r&&this._events.fire(\"helm:changed\",{helm:r,mol:e,source:n});}_restoreFromHistory(e,t){let n=this._service.serialize(this._mol),o=this._service.serialize(e);this._mol=e,this._resetLastAction(),this._events.fire(\"mol:changed\",{mol:e,changedAtomIds:new Set(e.atoms.map(r=>r.id)),changedBondIds:new Set(e.bonds.map(r=>r.id)),reason:t}),n!==o&&this._events.fire(\"helm:changed\",{helm:o,mol:e,source:t});}};function On(i){return i.startsWith(\"[\")&&i.endsWith(\"]\")||i.length===1&&/^[A-Za-z]$/.test(i)?i:`[${i}]`}function We(i,e,t){return `${On(i)}(${On(e)})${On(t)}`}function da(i,e){if(i===\"\")return `RNA1{${e}}$$$$V2.0`;let t=/(^|\\|)(RNA\\d+)\\{([^}]*)\\}/g,n=null,o;for(;(o=t.exec(i))!==null;)n={name:o[2],body:o[3],matchText:o[0]};if(n!==null){let h=n.body===\"\"?\"\":\".\",f=`${n.matchText.startsWith(\"|\")?\"|\":\"\"}${n.name}{${n.body}${h}${e}}`,y=i.lastIndexOf(n.matchText);return i.slice(0,y)+f+i.slice(y+n.matchText.length)}let r=new Set,s=/RNA(\\d+)\\{/g,a;for(;(a=s.exec(i))!==null;)r.add(Number(a[1]));let l=1;for(;r.has(l);)l+=1;let d=`RNA${l}{${e}}`,c=i.indexOf(\"$\");if(c<0)return `${i}|${d}$$$$V2.0`;let u=i.slice(0,c),m=i.slice(c);return `${u}${u===\"\"?\"\":\"|\"}${d}${m}`}var ca=5,ua=3,ma=14,pa=11,ha=9,fa=8,ba=48,ya=96;function ga(i){return i<=ua?ma:i<=6?pa:i<=9?ha:fa}function Ti(i,e){let t=$(e.monomer,e.biotype,e.theme.colorTheme),n=xt(t.background),o=t.text,r=Zn(o,n)<ca,s=e.monomer.symbol,a=ga(s.length),d=s.length>=10?\"line-height:1.1;letter-spacing:-0.02em;\":\"\",c=`font-size:${a}px;${d}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:${ya-16}px;display:inline-block;`,u=g(i,\"span\",{class:\"hw-palette__star\"},[e.favorite?\"\\u2605\":\"\\u2606\"]),m=g(i,\"span\",{class:\"hw-palette__label\",style:c},[s]),p=[\"hw-palette__tile\"];e.primed&&p.push(\"hw-palette__tile--primed\"),e.favorite&&p.push(\"hw-palette__tile--favorite\"),r&&p.push(\"hw-palette__tile--low-contrast\");let h=e.monomer.name!==void 0?`${s} \\u2014 ${e.monomer.name}`:s,f=`background:${n};color:${o};width:100%;min-width:${ba}px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return {root:g(i,\"div\",{class:p.join(\" \"),draggable:\"true\",role:\"button\",\"aria-pressed\":e.primed?\"true\":\"false\",\"aria-label\":h,\"data-symbol\":s,\"data-biotype\":e.biotype,\"data-bg\":n,\"data-raw-bg\":t.background,\"data-testid\":`palette-tile-${s}`,title:h,style:f},[u,m]),star:u}}function Si(i,e){let t=e.showStar!==false,n=g(i,\"span\",{class:\"hw-triplet-chip__star\"},[e.favorite?\"\\u2605\":\"\\u2606\"]),o=g(i,\"span\",{class:\"hw-triplet-chip__label\"},[e.label]),r=[\"hw-triplet-chip\"];e.favorite&&r.push(\"hw-triplet-chip--favorite\");let s=t?[n,o]:[o];return {root:g(i,\"div\",{class:r.join(\" \"),role:\"button\",tabindex:\"0\",\"aria-label\":e.title,\"data-sugar\":e.sugar,\"data-base\":e.base,\"data-linker\":e.linker,\"data-triplet\":e.label,\"data-testid\":`palette-triplet-${e.label}`,title:e.title,style:`background:${e.background};color:${e.textColor};`},s),star:n}}var ce=\"http://www.w3.org/2000/svg\",Ei={sugar:b.SUGAR,base:b.BASE,linker:b.LINKER},_a={sugar:[\"r\",\"R\"],base:[\"A\"],linker:[\"p\",\"P\"]},va=200,wa=180,st={x:70,y:60},Nn={x:140,y:60},Fn={x:70,y:130},je=18,Ci=18,at=22,Wt=class Wt{constructor(e,t,n){this.onValueSet=new Z;this.onPickModeChange=new Z;this._slots=new Map;this._favStar=null;this._pickMode=null;this._destroyed=false;this._builderRdkitCache=new Map;this._editor=t,this._doc=n?.documentImpl??S(e),this._hooks=n?.paletteHooks??null,this._favHooks=n?.favoriteHooks??null,this.element=g(this._doc,\"div\",{class:\"hw-rna-builder\",\"data-testid\":\"rna-builder\"});let o=g(this._doc,\"div\",{class:\"hw-rna-builder__header\"});if(o.appendChild(g(this._doc,\"div\",{class:\"hw-rna-builder__title\"},[\"RNA builder\"])),this._favHooks!==null){let l=g(this._doc,\"span\",{class:\"hw-rna-builder__fav hw-rna-builder__fav--disabled\",role:\"button\",tabindex:\"0\",\"data-testid\":\"rna-builder-fav-star\",title:\"Favorite this triplet\",\"aria-pressed\":\"false\",\"aria-disabled\":\"true\"},[\"\\u2606\"]),d=c=>{c.stopPropagation();let u=this.getSelection();u.preview===\"\"||this._favHooks===null||this._favHooks.toggleFavoriteTriplet(u.sugar,u.base,u.linker);};l.addEventListener(\"click\",d),l.addEventListener(\"keydown\",c=>{let u=c;(u.key===\"Enter\"||u.key===\" \")&&d(c);}),this._favStar=l,o.appendChild(l);}this.element.appendChild(o),this._hintEl=g(this._doc,\"div\",{class:\"hw-rna-builder__hint\",\"data-testid\":\"rna-builder-hint\",hidden:true}),this.element.appendChild(this._hintEl);let r=this._buildSvg();this.element.appendChild(r),this._preview=g(this._doc,\"div\",{class:\"hw-rna-builder__preview\",\"data-testid\":\"rna-builder-preview\"}),this.element.appendChild(this._preview),this._addBtn=g(this._doc,\"button\",{class:\"hw-rna-builder__add\",type:\"button\",\"data-testid\":\"rna-builder-add-btn\"},[\"Add triplet\"]),this._addBtn.addEventListener(\"click\",()=>this._onAddClicked()),this.element.appendChild(this._addBtn),e.appendChild(this.element);let s=t.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh();}),a=t.on(\"theme:change\",()=>{this._destroyed||this._repaintSlotColors();});this._libUnsub=()=>{try{s();}catch{}try{a();}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors();}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors();}getSelection(){let e=this._slots.get(\"sugar\")?.value??\"\",t=this._slots.get(\"base\")?.value??\"\",n=this._slots.get(\"linker\")?.value??\"\",o=e!==\"\"&&t!==\"\"&&n!==\"\"?We(e,t,n):\"\";return {sugar:e,base:t,linker:n,preview:o}}setField(e,t){let n=this._slots.get(e);n!==void 0&&(n.value=t,this._setLabelText(n.labelEl,t),this._repaintSlot(n),this._updatePreview(),this.onValueSet.next({field:e,symbol:t}));}startPickMode(e){if(this._pickMode===e){this.cancelPickMode();return}this._pickMode!==null&&this._setSlotPressed(this._pickMode,false),this._pickMode=e,this._setSlotPressed(e,true),this._setHintActive(e),this.onPickModeChange.next({field:e}),this._hooks!==null&&this._hooks.beginBiotypeFilter(Ei[e],t=>{this.setField(e,t),this._exitPickMode();},()=>{this._exitPickMode();});}cancelPickMode(){this._pickMode!==null&&(this._hooks!==null&&this._hooks.endBiotypeFilter(),this._exitPickMode());}getPickMode(){return this._pickMode}triggerAdd(){this._onAddClicked();}destroy(){this._destroyed||(this._destroyed=true,this._pickMode!==null&&this._hooks!==null&&this._hooks.endBiotypeFilter(),this._libUnsub(),this.onValueSet.complete(),this.onPickModeChange.complete(),this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element));}_buildSvg(){let e=this._doc.createElementNS(ce,\"svg\");e.setAttribute(\"class\",\"hw-rna-builder__triplet\"),e.setAttribute(\"viewBox\",`0 0 ${va} ${wa}`),e.setAttribute(\"data-testid\",\"rna-builder-triplet-svg\"),e.setAttribute(\"role\",\"group\"),e.setAttribute(\"aria-label\",\"Triplet preview\");let t=this._doc.createElementNS(ce,\"line\");t.setAttribute(\"class\",\"hw-rna-builder__bond\"),t.setAttribute(\"x1\",String(st.x+je)),t.setAttribute(\"y1\",String(st.y)),t.setAttribute(\"x2\",String(Nn.x-Ci)),t.setAttribute(\"y2\",String(Nn.y)),e.appendChild(t);let n=this._doc.createElementNS(ce,\"line\");n.setAttribute(\"class\",\"hw-rna-builder__bond\"),n.setAttribute(\"x1\",String(st.x)),n.setAttribute(\"y1\",String(st.y+je)),n.setAttribute(\"x2\",String(Fn.x)),n.setAttribute(\"y2\",String(Fn.y-at)),e.appendChild(n);let o=this._doc.createElementNS(ce,\"rect\");o.setAttribute(\"class\",\"hw-rna-builder__slot-shape\"),o.setAttribute(\"x\",String(-je)),o.setAttribute(\"y\",String(-je)),o.setAttribute(\"width\",String(je*2)),o.setAttribute(\"height\",String(je*2)),o.setAttribute(\"rx\",\"8\"),o.setAttribute(\"ry\",\"8\");let r=this._buildSlot(\"sugar\",\"Pick sugar (backbone)\",st,o),s=this._doc.createElementNS(ce,\"circle\");s.setAttribute(\"class\",\"hw-rna-builder__slot-shape\"),s.setAttribute(\"cx\",\"0\"),s.setAttribute(\"cy\",\"0\"),s.setAttribute(\"r\",String(Ci));let a=this._buildSlot(\"linker\",\"Pick linker\",Nn,s),l=this._doc.createElementNS(ce,\"path\");l.setAttribute(\"class\",\"hw-rna-builder__slot-shape\"),l.setAttribute(\"d\",`M ${-at} 0 L 0 ${-at} L ${at} 0 L 0 ${at} Z`);let d=this._buildSlot(\"base\",\"Pick base\",Fn,l);return e.appendChild(a.groupEl),e.appendChild(r.groupEl),e.appendChild(d.groupEl),this._slots.set(\"sugar\",r),this._slots.set(\"linker\",a),this._slots.set(\"base\",d),e}_buildSlot(e,t,n,o){let r=this._doc.createElementNS(ce,\"g\");r.setAttribute(\"class\",\"hw-rna-builder__slot\"),r.setAttribute(\"data-slot\",e),r.setAttribute(\"data-testid\",`rna-builder-slot-${e}`),r.setAttribute(\"role\",\"button\"),r.setAttribute(\"tabindex\",\"0\"),r.setAttribute(\"aria-label\",t),r.setAttribute(\"aria-pressed\",\"false\"),r.setAttribute(\"transform\",`translate(${n.x} ${n.y})`),r.appendChild(o);let s=this._doc.createElementNS(ce,\"text\");s.setAttribute(\"class\",\"hw-rna-builder__slot-label\"),s.setAttribute(\"data-testid\",`rna-builder-${e}-value`),s.setAttribute(\"x\",\"0\"),s.setAttribute(\"y\",\"0\"),s.setAttribute(\"text-anchor\",\"middle\"),s.setAttribute(\"dominant-baseline\",\"central\"),r.appendChild(s);let a=l=>{l.stopPropagation(),this.startPickMode(e);};return r.addEventListener(\"click\",a),r.addEventListener(\"keydown\",l=>{let d=l;(d.key===\"Enter\"||d.key===\" \")&&a(l);}),r.addEventListener(\"mouseenter\",l=>this._showSlotTooltip(e,l)),r.addEventListener(\"mouseleave\",()=>this._hideSlotTooltip()),r.addEventListener(\"focus\",()=>this._showSlotTooltip(e,null)),r.addEventListener(\"blur\",()=>this._hideSlotTooltip()),{id:e,biotype:Ei[e],groupEl:r,shapeEl:o,labelEl:s,value:\"\"}}_setLabelText(e,t){let n=[];for(let a=e.firstChild;a!==null;a=a.nextSibling)a.nodeName===\"title\"||a.nodeName===\"TITLE\"||n.push(a);for(let a of n)e.removeChild(a);let o=xa(t);e.setAttribute(\"font-size\",String(o)),e.setAttribute(\"text-anchor\",\"middle\"),e.setAttribute(\"dominant-baseline\",\"central\");let r=t.length>10?`${t.slice(0,9)}\\u2026`:t;e.appendChild(this._doc.createTextNode(r));let s=e.parentNode;if(s!==null){let a=null;for(let l=s.firstChild;l!==null;l=l.nextSibling)if(l.nodeName===\"title\"||l.nodeName===\"TITLE\"){a=l;break}for(a===null&&(a=this._doc.createElementNS(ce,\"title\"),s.insertBefore(a,s.firstChild));a.firstChild!==null;)a.removeChild(a.firstChild);a.appendChild(this._doc.createTextNode(t));}}_repaintSlotColors(){for(let e of this._slots.values())this._repaintSlot(e);}_repaintSlot(e){let t=this._editor.getService().monomerLib,n=this._theme(),o=e.value===\"\"?null:Ma(t,e.biotype,e.value),r=$(o,e.biotype,n.colorTheme);e.shapeEl.style.fill=r.background,e.shapeEl.style.stroke=r.line,e.labelEl.style.fill=r.text;}_populateDefaults(){let e=this._editor.getService().monomerLib;for(let[t,n]of this._slots.entries()){let o=ka(e,n.biotype),r=Aa(o,_a[t]),s=n.value!==\"\"&&o.some(a=>a.symbol===n.value)?n.value:r??o[0]?.symbol??\"\";n.value=s,this._setLabelText(n.labelEl,s);}}_updatePreview(){let e=this.getSelection();for(;this._preview.firstChild!==null;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(e.preview===\"\"?\"-\":e.preview)),this._updateFavStar(e);}_updateFavStar(e){if(this._favStar===null||this._favHooks===null)return;let t=e.preview!==\"\",n=t&&this._favHooks.isFavoriteTriplet(e.sugar,e.base,e.linker);for(;this._favStar.firstChild!==null;)this._favStar.removeChild(this._favStar.firstChild);this._favStar.appendChild(this._doc.createTextNode(n?\"\\u2605\":\"\\u2606\")),this._favStar.setAttribute(\"aria-pressed\",n?\"true\":\"false\"),t?this._favStar.removeAttribute(\"aria-disabled\"):this._favStar.setAttribute(\"aria-disabled\",\"true\");let o=\"hw-rna-builder__fav\"+(n?\" hw-rna-builder__fav--active\":\"\")+(t?\"\":\" hw-rna-builder__fav--disabled\");this._favStar.setAttribute(\"class\",o);}_onAddClicked(){let e=this.getSelection();e.preview!==\"\"&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker);}_exitPickMode(){if(this._pickMode===null)return;let e=this._pickMode;this._setSlotPressed(e,false),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null});}_setHintActive(e){let t=this._hintEl;for(;t.firstChild!==null;)t.removeChild(t.firstChild);if(e===null){t.setAttribute(\"hidden\",\"\");return}t.removeAttribute(\"hidden\");let n=e===\"sugar\"?\"sugar\":e===\"base\"?\"base\":\"linker\";t.appendChild(this._doc.createTextNode(`Pick ${n} from palette`));}_setSlotPressed(e,t){let n=this._slots.get(e);if(n===void 0)return;n.groupEl.setAttribute(\"aria-pressed\",t?\"true\":\"false\");let r=(n.groupEl.getAttribute(\"class\")??\"\").split(/\\s+/).filter(s=>s!==\"hw-rna-builder__slot--active\").join(\" \");n.groupEl.setAttribute(\"class\",t?`${r} hw-rna-builder__slot--active`:r);}_theme(){let e=this._editor;return typeof e._currentTheme==\"function\"?e._currentTheme():this._editor.getService().theme}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_builderRdkitSvgFor(e){if(e===null)return null;let t=e.smiles;if(t===void 0||t===\"\")return null;let n=this._rdkit();if(n===null)return null;let o=`${e.polymerType}:${e.symbol}`;if(this._builderRdkitCache.has(o))return this._builderRdkitCache.get(o)??null;let r=ye(n,t,220,140);if(this._builderRdkitCache.size>=Wt._BUILDER_RDKIT_CACHE_LIMIT){let s=this._builderRdkitCache.keys().next().value;s!==void 0&&this._builderRdkitCache.delete(s);}return this._builderRdkitCache.set(o,r),r}_slotHint(e){switch(e){case \"sugar\":return \"Click to choose a different sugar\";case \"base\":return \"Click to choose a different base\";case \"linker\":return \"Click to choose a different linker\"}}_slotTitle(e,t){let n=t===\"\"?\"?\":t;switch(e){case \"sugar\":return `Sugar: ${n}`;case \"base\":return `Base: ${n}`;case \"linker\":return `Linker: ${n}`}}_showSlotTooltip(e,t){let n=this._slots.get(e);if(n===void 0)return;let r=this._editor.getService().monomerLib.getMonomerSet(n.biotype),s=n.value===\"\"?null:r.get(n.value)??null,a=oe(this._doc,\"builder-tooltip\",\"hw-builder-tooltip\");Me(this._doc,a,{symbol:this._slotTitle(e,n.value),name:s?.name??\"\",rdkitSvg:this._builderRdkitSvgFor(s),rdkitTestid:\"builder-tooltip-rdkit-svg\",hint:this._slotHint(e)});let l=t;if(l!==null&&typeof l.clientX==\"number\"&&typeof l.clientY==\"number\")Y(a,l.clientX,l.clientY);else {let d=n.groupEl,c=typeof d.getBoundingClientRect==\"function\"?d.getBoundingClientRect():null;c!==null?Y(a,c.left+c.width/2,c.top+c.height/2):Y(a,0,0);}}_hideSlotTooltip(){let e=this._doc.body.querySelector('[data-testid=\"builder-tooltip\"]');V(e);}};Wt._BUILDER_RDKIT_CACHE_LIMIT=256;var Kt=Wt;function xa(i){let e=i.length;return e<=2?16:e<=4?11:e<=7?8:e<=10?6:5}function ka(i,e){let t=i.getMonomerSet(e),n=[];for(let o of t.values())n.push(o);return n.sort((o,r)=>o.symbol.localeCompare(r.symbol)),n}function Aa(i,e){let t=new Set;for(let n of i)t.add(n.symbol);for(let n of e)if(t.has(n))return n;return null}function Ma(i,e,t){return i.getMonomerSet(e).get(t)??null}var ue=\"Favorites\",Gn={[ue]:\"\\u2605 Favorites\",[v.PEPTIDE]:\"Peptides\",[v.RNA]:\"RNA\",[v.CHEM]:\"CHEM\",[v.BLOB]:\"BLOB\",G:\"G\"},jt=[ue,v.PEPTIDE,v.RNA,v.CHEM,v.BLOB,\"G\"],Li=\"hwe:palette:favorites\",Bi=\"hwe:palette:active-tab\",Ta=\"hwe.palette.favorites\";function qt(i){return `${i.sugar}|${i.base}|${i.linker}`}var qe=class qe{constructor(e,t,n){this.favoritesChanged=new Z;this._nextAddUnsub=()=>{};this._favorites=new Set;this._favoriteTriplets=[];this._pendingRnaSelection=null;this._visibleTabs=[ue];this._activeTab=ue;this._searchInput=null;this._filter=\"\";this._destroyed=false;this._rnaBuilder=null;this._activeBiotypeFilter=null;this._pickResolver=null;this._pickCanceller=null;this._pickEscapeListener=null;this._pickOutsideClickListener=null;this._paletteRdkitCache=new Map;this._editor=t,this._doc=n?.documentImpl??S(e),this._opts={documentImpl:this._doc,groupByNaturalAnalog:n?.groupByNaturalAnalog??true,allowFavorites:n?.allowFavorites??true},this._loadFavorites(),this._activeTab=this._resolveInitialTab(n?.initialTab),this.element=g(this._doc,\"div\",{class:\"hw-palette\",\"data-testid\":\"palette\"}),e.appendChild(this.element),this._render(),this._libUnsub=t.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh();}),this._themeUnsub=t.on(\"theme:change\",()=>{this._destroyed||this.refresh();}),this._nextAddUnsub=t.on(\"option:change\",o=>{this._destroyed||o.key===\"nextAdd\"&&this._updatePrimedClasses();});}refresh(){this._render();}setFilter(e){this._filter=e.trim().toLowerCase(),this._searchInput!==null&&this._searchInput.value!==e&&(this._searchInput.value=e),this._applyFilter();}setActiveTab(e){this._visibleTabs.includes(e)&&(this._activeTab=e,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter());}getActiveTab(){return this._activeTab}getFavorites(){let e=this._editor.getService().monomerLib,t=[];for(let n of this._favorites)this._findMonomer(e,n)!==null&&t.push(n);return t}setFavorite(e,t){let n=this._favorites.has(e);t!==n&&(t?this._favorites.add(e):this._favorites.delete(e),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged());}clearFavorites(){this._favorites.size===0&&this._favoriteTriplets.length===0||(this._favorites.clear(),this._favoriteTriplets.length=0,this._saveFavorites(),this._render(),this._emitFavoritesChanged());}getFavoriteTriplets(){return this._favoriteTriplets.map(e=>({...e}))}isFavoriteTriplet(e,t,n){let o=qt({sugar:e,base:t,linker:n});return this._favoriteTriplets.some(r=>qt(r)===o)}setFavoriteTriplet(e,t,n,o){let r=qt({sugar:e,base:t,linker:n}),s=this._favoriteTriplets.findIndex(l=>qt(l)===r),a=s>=0;o!==a&&(o?this._favoriteTriplets.push({sugar:e,base:t,linker:n}):this._favoriteTriplets.splice(s,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged());}_hidePaletteTooltips(){let e=this._doc.body;V(e.querySelector('[data-testid=\"palette-tooltip\"]')),V(e.querySelector('[data-testid=\"palette-triplet-tooltip\"]'));}_emitFavoritesChanged(){this.favoritesChanged.next({favorites:this.getFavorites(),triplets:this.getFavoriteTriplets()});}destroy(){this._destroyed||(this._destroyed=true,this._rnaBuilder!==null&&(this._rnaBuilder.destroy(),this._rnaBuilder=null),this._libUnsub(),this._themeUnsub(),this._nextAddUnsub(),this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element));}getRnaBuilder(){return this._rnaBuilder}hasActiveBiotypeFilter(){return this._activeBiotypeFilter!==null}getActiveBiotypeFilter(){return this._activeBiotypeFilter}cancelBiotypeFilter(){if(this._activeBiotypeFilter===null)return;let e=this._pickCanceller;this._teardownPickMode(),e?.();}_buildPaletteFilterHooks(){return {beginBiotypeFilter:(e,t,n)=>{this._activeBiotypeFilter!==null&&this._teardownPickMode(),this._activeBiotypeFilter=e,this._pickResolver=t,this._pickCanceller=n,this._applyFilter();let o=l=>{l.key===\"Escape\"&&this.cancelBiotypeFilter();};this._pickEscapeListener=o,this._doc.defaultView?.addEventListener(\"keydown\",o);let s=l=>{if(this._activeBiotypeFilter===null)return;let d=l.target;if(d==null)return;let c=this._activeBiotypeFilter,u=d;for(;u!==null;){let m=u.getAttribute===void 0?null:u.getAttribute(\"class\");if(m!==null){let p=m.split(/\\s+/);if(p.includes(\"hw-palette__tile\")){if((u.getAttribute(\"data-biotype\")??\"\")===c)return;break}if(p.includes(\"hw-rna-builder__slot\")){if(this._isInsideOwnPalette(u))return;break}}u=u.parentElement;}this.cancelBiotypeFilter();};this._pickOutsideClickListener=s,this._doc.addEventListener(\"mousedown\",s,true);},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let e=this.element.querySelector(`.hw-palette__pane[data-tab=\"${this._activeTab}\"]`);if(e===null)return;let t=e;try{if(typeof t.scrollTo==\"function\"){t.scrollTo({top:0,behavior:\"smooth\"});return}}catch{}typeof t.scrollTop==\"number\"&&(t.scrollTop=0);}_isInsideOwnPalette(e){let t=e;for(;t!==null;){if(t===this.element)return  true;t=t.parentElement;}return  false}_teardownPickMode(){this._activeBiotypeFilter!==null&&(this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,this._pickEscapeListener!==null&&(this._doc.defaultView?.removeEventListener(\"keydown\",this._pickEscapeListener),this._pickEscapeListener=null),this._pickOutsideClickListener!==null&&(this._doc.removeEventListener(\"mousedown\",this._pickOutsideClickListener,true),this._pickOutsideClickListener=null),this._applyFilter());}_render(){for(this._rnaBuilder!==null&&(this._pendingRnaSelection=this._rnaBuilder.getSelection(),this._rnaBuilder.destroy(),this._rnaBuilder=null);this.element.firstChild!==null;)this.element.removeChild(this.element.firstChild);let e=this._doc.createElement(\"input\");e.setAttribute(\"type\",\"search\"),e.setAttribute(\"class\",\"hw-palette__search\"),e.setAttribute(\"placeholder\",\"Search monomers...\"),e.setAttribute(\"data-testid\",\"palette-search\"),this._filter!==\"\"&&(e.value=this._filter),e.addEventListener(\"input\",()=>this.setFilter(e.value)),this._searchInput=e,this.element.appendChild(e),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=ue);let t=g(this._doc,\"div\",{class:\"hw-palette__tabs\",role:\"tablist\",\"data-testid\":\"palette-tabs\"});for(let s of this._visibleTabs){let a=s===this._activeTab,l=g(this._doc,\"button\",{class:\"hw-palette__tab\",type:\"button\",role:\"tab\",\"aria-controls\":`hw-palette-pane-${s}`,\"aria-selected\":a?\"true\":\"false\",\"data-testid\":`palette-tab-${s}`,\"data-tab\":s,title:Gn[s]},[Gn[s]]);l.addEventListener(\"click\",()=>this.setActiveTab(s)),t.appendChild(l);}this.element.appendChild(t);let n=g(this._doc,\"div\",{class:\"hw-palette__panes\"}),o=this._theme(),r=this._editor.getService().monomerLib;for(let s of this._visibleTabs){let a=s===this._activeTab,l=g(this._doc,\"div\",{class:\"hw-palette__pane\",id:`hw-palette-pane-${s}`,role:\"tabpanel\",\"data-testid\":`palette-pane-${s}`,\"data-tab\":s,hidden:!a});s===ue?this._buildFavoritesPane(l,r,o):this._buildPolymerPane(l,s,r,o),n.appendChild(l);}this.element.appendChild(n),this._applyFilter();}_computeVisibleTabs(){let e=this._editor.getService().monomerLib,t=new Set;for(let o of e.getPolymerTypes())t.add(o);let n=[];n.push(ue);for(let o of jt)o!==ue&&t.has(o)&&n.push(o);return n}_buildFavoritesPane(e,t,n){let o=this._resolveFavoriteMonomers(t),r=this._favoriteTriplets;if(o.length===0&&r.length===0){let s=g(this._doc,\"div\",{class:\"hw-palette__placeholder\",\"data-testid\":\"palette-favorites-empty\"},[\"No favorites yet \\u2014 click the \\u2606 on any tile to add one.\"]);e.appendChild(s);return}for(let[s,a]of this._groupByPolymerAndType(o))e.appendChild(this._renderGroup(s,a));r.length>0&&e.appendChild(this._renderTripletGroup(\"RNA \\xB7 Triplets\",r,t));}_groupByPolymerAndType(e){let t=new Map;for(let s of e){let a=s.polymerType,l=s.monomerType??\"Undefined\",d=`${a}|${l}`,c=t.get(d);c===void 0&&(c={pt:a,mt:l,list:[]},t.set(d,c)),c.list.push(s);}let n=s=>{let a=jt.indexOf(s);return a<0?99:a},o={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(t.values()).sort((s,a)=>n(s.pt)-n(a.pt)||(o[s.mt]??9)-(o[a.mt]??9)||s.mt.localeCompare(a.mt)).map(s=>[`${this._polymerLabel(s.pt)} \\xB7 ${s.mt}`,s.list])}_polymerLabel(e){return Gn[e]??e}_renderTripletGroup(e,t,n){let o=g(this._doc,\"div\",{class:\"hw-palette__group\",\"data-natural-analog\":e}),r=g(this._doc,\"div\",{class:\"hw-palette__group-header\",\"data-testid\":`palette-group-${e}`},[e]),s=g(this._doc,\"div\",{class:\"hw-triplet-chips\",\"data-testid\":\"palette-triplet-favorites\"});for(let a of t)s.appendChild(this._renderTripletChip(a,n));return o.appendChild(r),o.appendChild(s),o}_renderTripletChip(e,t){let n=We(e.sugar,e.base,e.linker),o=t.getMonomerSet(b.BASE).get(e.base)??null,r=$(o,b.BASE,this._theme().colorTheme),s=this.isFavoriteTriplet(e.sugar,e.base,e.linker),a=o?.name!==void 0&&o.name!==\"\"?`${n} \\u2014 ${o.name}`:n,{root:l}=Si(this._doc,{sugar:e.sugar,base:e.base,linker:e.linker,label:n,title:a,background:xt(r.background),textColor:r.text,favorite:s,showStar:this._opts.allowFavorites});return this._wireTripletChip(l,e),l}_wireTripletChip(e,t){e.addEventListener(\"mouseenter\",n=>{let o=n,r=oe(this._doc,\"palette-triplet-tooltip\",\"hw-palette-tooltip hw-triplet-tooltip\");mi(this._doc,r,{title:We(t.sugar,t.base,t.linker),parts:this._tripletTooltipParts(t),hint:\"Click to add this triplet\",rdkitTestid:\"palette-triplet-tooltip-rdkit-svg\"}),Y(r,typeof o.clientX==\"number\"?o.clientX:0,typeof o.clientY==\"number\"?o.clientY:0);}),e.addEventListener(\"mouseleave\",()=>{V(this._doc.body.querySelector('[data-testid=\"palette-triplet-tooltip\"]'));}),e.addEventListener(\"click\",n=>{let o=n.target;if(this._opts.allowFavorites&&o?.classList?.contains(\"hw-triplet-chip__star\")===true){this.setFavoriteTriplet(t.sugar,t.base,t.linker,!this.isFavoriteTriplet(t.sugar,t.base,t.linker)),n.stopPropagation();return}this._editor.placeRnaTriplet(t.sugar,t.base,t.linker);}),e.addEventListener(\"keydown\",n=>{let o=n;(o.key===\"Enter\"||o.key===\" \")&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker);});}_buildRnaDefaultChips(e){let t=this._pickSymbol(e.getMonomerSet(b.SUGAR),[\"r\",\"R\"]),n=this._pickSymbol(e.getMonomerSet(b.LINKER),[\"p\",\"P\"]),o=e.getMonomerSet(b.BASE);if(t===null||n===null)return null;let r=qe._DEFAULT_TRIPLET_BASES.filter(a=>o.has(a));if(r.length===0)return null;let s=g(this._doc,\"div\",{class:\"hw-triplet-chips hw-triplet-chips--defaults\",\"data-testid\":\"rna-default-triplets\"});for(let a of r)s.appendChild(this._renderTripletChip({sugar:t,base:a,linker:n},e));return s}_tripletTooltipParts(e){let t=this._editor.getService().monomerLib,n=(o,r,s)=>{let a=t.getMonomerSet(r).get(s)??null;return {role:o,symbol:s,...a?.name!==void 0?{name:a.name}:{},rdkitSvg:a===null?null:this._paletteRdkitSvg(a)}};return [n(\"Sugar\",b.SUGAR,e.sugar),n(\"Base\",b.BASE,e.base),n(\"Linker\",b.LINKER,e.linker)]}_pickSymbol(e,t){for(let o of t)if(e.has(o))return o;let n=e.keys().next();return n.done===true?null:n.value}_restoreRnaSelection(){let e=this._pendingRnaSelection;if(this._pendingRnaSelection=null,e===null||this._rnaBuilder===null)return;let t=this._editor.getService().monomerLib;e.sugar!==\"\"&&t.getMonomerSet(b.SUGAR).has(e.sugar)&&this._rnaBuilder.setField(\"sugar\",e.sugar),e.base!==\"\"&&t.getMonomerSet(b.BASE).has(e.base)&&this._rnaBuilder.setField(\"base\",e.base),e.linker!==\"\"&&t.getMonomerSet(b.LINKER).has(e.linker)&&this._rnaBuilder.setField(\"linker\",e.linker);}_resolveFavoriteMonomers(e){let t=[];for(let n of this._favorites){let o=this._findMonomer(e,n);o!==null&&t.push(o);}return t}_findMonomer(e,t){for(let n of e.getPolymerTypes()){let o=e.getMonomer(n,t);if(o!==null)return o}return null}_buildPolymerPane(e,t,n,o){let r=t,s=this._monomersForPolymer(r,n);if(s.length===0)return;if(r===v.RNA){this._rnaBuilder=new Kt(e,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(m,p,h)=>this.isFavoriteTriplet(m,p,h),toggleFavoriteTriplet:(m,p,h)=>this.setFavoriteTriplet(m,p,h,!this.isFavoriteTriplet(m,p,h))}:null}),this._restoreRnaSelection();let c=this._buildRnaDefaultChips(n);c!==null&&e.appendChild(c);let u=this._groupRna(s);for(let[m,p]of u)p.length!==0&&e.appendChild(this._renderGroup(m,p));return}if(r===v.PEPTIDE&&this._opts.groupByNaturalAnalog){let c=this._groupByAnalog(s);for(let[u,m]of c){let p=u===\"\"?\"Other\":u;e.appendChild(this._renderGroup(p,m));}return}let a=g(this._doc,\"div\",{class:\"hw-palette__group-tiles\"}),l=this._editor.getNextAddSymbol(),d=this._sortByColor(s);for(let c of d){let u=this._biotype(c,r);a.appendChild(this._renderTile(c,u,l));}e.appendChild(a);}_renderGroup(e,t){let n=g(this._doc,\"div\",{class:\"hw-palette__group\",\"data-natural-analog\":e}),o=g(this._doc,\"div\",{class:\"hw-palette__group-header\",\"data-testid\":`palette-group-${e}`},[e]),r=g(this._doc,\"div\",{class:\"hw-palette__group-tiles\"}),s=this._editor.getNextAddSymbol(),a=this._sortByColor(t);for(let l of a){let d=this._biotype(l,l.polymerType);r.appendChild(this._renderTile(l,d,s));}return n.appendChild(o),n.appendChild(r),n}_sortByColor(e){let t=this._theme(),n=e.map((o,r)=>{let s=this._biotype(o,o.polymerType),a=$(o,s,t.colorTheme),l=Qn(a.background),d=l.s===0?1:0;return {m:o,idx:r,h:l.h,s:l.s,l:l.l,isGrey:d}});return n.sort((o,r)=>o.isGrey!==r.isGrey?o.isGrey-r.isGrey:o.h!==r.h?o.h-r.h:o.s!==r.s?o.s-r.s:o.l!==r.l?o.l-r.l:o.idx-r.idx),n.map(o=>o.m)}_monomersForPolymer(e,t){let n=t.getMonomerSymbolsByType(e),o=[];for(let r of n){let s=t.getMonomer(e,r);s!==null&&o.push(s);}return o.sort((r,s)=>r.symbol.localeCompare(s.symbol)),o}_groupByAnalog(e){let t=new Map;for(let r of e){let s=r.naturalAnalog??\"\",a=t.get(s);a===void 0&&(a=[],t.set(s,a)),a.push(r);}let n=[],o=Array.from(t.keys()).sort((r,s)=>r===\"\"&&s!==\"\"?1:s===\"\"&&r!==\"\"?-1:r.localeCompare(s));for(let r of o)n.push([r,t.get(r)]);return new Map(n)}_groupRna(e){let t=[],n=[],o=[],r=[];for(let a of e){let l=ee(a);l===b.SUGAR?t.push(a):l===b.BASE?n.push(a):l===b.LINKER?o.push(a):r.push(a);}let s=new Map;return s.set(\"Backbones\",t),s.set(\"Bases\",n),s.set(\"Linkers\",o),r.length>0&&s.set(\"Other\",r),s}_renderTile(e,t,n){let o=this._favorites.has(e.symbol),r=n!==null&&n.symbol===e.symbol&&n.biotype===t,{root:s,star:a}=Ti(this._doc,{monomer:e,biotype:t,theme:this._theme(),favorite:o,primed:r});return this._wireTile(s,a,e,t),s}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_paletteRdkitSvg(e){let t=e.smiles;if(t===void 0||t===\"\")return null;let n=this._rdkit();if(n===null)return null;let o=`${e.polymerType}:${e.symbol}`;if(this._paletteRdkitCache.has(o))return this._paletteRdkitCache.get(o)??null;let r=ye(n,t,220,140);if(this._paletteRdkitCache.size>=qe._PALETTE_RDKIT_CACHE_LIMIT){let s=this._paletteRdkitCache.keys().next().value;s!==void 0&&this._paletteRdkitCache.delete(s);}return this._paletteRdkitCache.set(o,r),r}_wireTile(e,t,n,o){e.addEventListener(\"mouseenter\",r=>{let s=r,a=oe(this._doc,\"palette-tooltip\",\"hw-palette-tooltip\");Me(this._doc,a,{symbol:n.symbol,name:n.name??\"\",rdkitSvg:this._paletteRdkitSvg(n),rdkitTestid:\"palette-tooltip-rdkit-svg\"});let l=typeof s.clientX==\"number\"?s.clientX:0,d=typeof s.clientY==\"number\"?s.clientY:0;Y(a,l,d);}),e.addEventListener(\"mouseleave\",()=>{V(this._doc.body.querySelector('[data-testid=\"palette-tooltip\"]'));}),e.addEventListener(\"click\",r=>{let s=r.target;if(this._opts.allowFavorites&&s!==void 0&&s?.classList?.contains(\"hw-palette__star\")===true){this.setFavorite(n.symbol,!this._favorites.has(n.symbol)),r.stopPropagation();return}if(this._activeBiotypeFilter!==null&&this._activeBiotypeFilter===o){let d=this._pickResolver;this._teardownPickMode(),d?.(n.symbol),this._scrollActivePaneToTop(),r.stopPropagation();return}let a=this._editor.getSelection();if(a.atoms.size>0){let d=this._editor.getMol(),c=[];for(let m of a.atoms){let p=d.atoms.find(h=>h.id===m);p!==void 0&&c.push(p);}if(c.length>0&&c.every(m=>m.biotype===o)){this._editor.replaceMonomers(c,n.symbol),r.stopPropagation();return}this._editor.fire(\"editor:status\",{message:`Cannot bulk-replace ${c.length} selected atom(s) with ${n.symbol}: selection contains incompatible biotypes for ${o}.`,severity:\"warn\",durationMs:3e3}),r.stopPropagation();return}let l=this._editor.getNextAddSymbol();if(l!==null&&l.symbol===n.symbol&&l.biotype===o){this._editor.setNextAddSymbol(null),this._updatePrimedClasses();return}this._editor.setNextAddSymbol(n.symbol,o),this._updatePrimedClasses();}),e.addEventListener(\"dragstart\",r=>{let s=r.dataTransfer;if(s!=null)try{s.setData(\"application/x-hwe-monomer\",JSON.stringify({symbol:n.symbol,biotype:o})),s.effectAllowed=\"copy\";}catch{}V(this._doc.body.querySelector('[data-testid=\"palette-tooltip\"]')),this._editor.startPaletteDrag(n.symbol,o);});}_biotype(e,t){let n=ee(e);if(n!==null)return n;switch(t){case v.PEPTIDE:return b.AA;case v.RNA:return b.SUGAR;case v.CHEM:return b.CHEM;case v.BLOB:return b.BLOB;default:return b.CHEM}}_theme(){let e=this._editor;return typeof e._currentTheme==\"function\"?e._currentTheme():this._editor.getService().theme}_applyFilter(){let e=this._filter,t=this._activeBiotypeFilter,n=this.element.querySelector(`.hw-palette__pane[data-tab=\"${this._activeTab}\"]`),o=(n??this.element).querySelectorAll(\".hw-palette__tile\");for(let a=0;a<o.length;a++){let l=o[a],d=(l.getAttribute(\"data-symbol\")??\"\").toLowerCase(),c=(l.getAttribute(\"title\")??\"\").toLowerCase(),u=l.getAttribute(\"data-biotype\")??\"\",h=(e===\"\"||d.indexOf(e)>=0||c.indexOf(e)>=0)&&(t===null||u===t);l.style.display=h?\"\":\"none\";}let r=(n??this.element).querySelectorAll(\".hw-triplet-chip\");for(let a=0;a<r.length;a++){let l=r[a],d=[l.getAttribute(\"data-triplet\")??\"\",l.getAttribute(\"data-sugar\")??\"\",l.getAttribute(\"data-base\")??\"\",l.getAttribute(\"data-linker\")??\"\"].join(\" \").toLowerCase(),c=(e===\"\"||d.indexOf(e)>=0)&&t===null;l.style.display=c?\"\":\"none\";}let s=(n??this.element).querySelectorAll(\".hw-palette__group\");for(let a=0;a<s.length;a++){let l=s[a],d=l.querySelectorAll(\".hw-palette__tile, .hw-triplet-chip\"),c=false;for(let u=0;u<d.length;u++)if(d[u].style.display!==\"none\"){c=true;break}c?(l.removeAttribute(\"hidden\"),l.removeAttribute(\"data-section-empty\")):(l.setAttribute(\"hidden\",\"\"),l.setAttribute(\"data-section-empty\",\"true\"));}}_updatePrimedClasses(){let e=this._editor.getNextAddSymbol(),t=this.element.querySelectorAll(\".hw-palette__tile\");for(let n=0;n<t.length;n++){let o=t[n],r=o.getAttribute(\"data-symbol\")??\"\",s=o.getAttribute(\"data-biotype\")??\"\",a=e!==null&&e.symbol===r&&e.biotype===s,d=(o.getAttribute(\"class\")??\"\").split(/\\s+/).filter(c=>c!==\"hw-palette__tile--primed\").join(\" \");o.setAttribute(\"class\",a?`${d} hw-palette__tile--primed`:d),o.setAttribute(\"aria-pressed\",a?\"true\":\"false\");}}_applyActiveTabClasses(){let e=this.element.querySelectorAll(\".hw-palette__tab\");for(let n=0;n<e.length;n++){let o=e[n],r=o.getAttribute(\"data-tab\")??\"\";o.setAttribute(\"aria-selected\",r===this._activeTab?\"true\":\"false\");}let t=this.element.querySelectorAll(\".hw-palette__pane\");for(let n=0;n<t.length;n++){let o=t[n];(o.getAttribute(\"data-tab\")??\"\")===this._activeTab?o.removeAttribute(\"hidden\"):o.setAttribute(\"hidden\",\"\");}}_localStorage(){if(!this._opts.allowFavorites)return null;let e=this._doc.defaultView;if(e==null)return null;try{return e.localStorage??null}catch{return null}}_resolveInitialTab(e){if(e!==void 0&&jt.includes(e))return e;let t=this._localStorage();if(t!==null)try{let n=t.getItem(Bi);if(n!==null&&jt.includes(n))return n}catch{}return ue}_persistActiveTab(){let e=this._localStorage();if(e!==null)try{e.setItem(Bi,this._activeTab);}catch{}}_loadFavorites(){let e=this._localStorage();if(e!==null){try{let t=e.getItem(Li);if(t!==null&&t!==\"\"){let n=JSON.parse(t),o=this._extractSymbols(n);for(let r of o)this._favorites.add(r);for(let r of this._extractTriplets(n))this._favoriteTriplets.push(r);return}}catch{}try{let t=e.getItem(Ta);if(t===null||t===\"\")return;let n=JSON.parse(t);if(Array.isArray(n)){for(let o of n){if(typeof o!=\"string\")continue;let r=o.indexOf(\"|\"),s=r>=0?o.slice(r+1):o;s!==\"\"&&this._favorites.add(s);}this._saveFavorites();}}catch{}}}_extractSymbols(e){if(Array.isArray(e)){let t=[];for(let n of e)typeof n==\"string\"&&t.push(n);return t}if(e!==null&&typeof e==\"object\"){let t=e;if(Array.isArray(t.symbols)){let n=[];for(let o of t.symbols)typeof o==\"string\"&&n.push(o);return n}}return []}_extractTriplets(e){if(e===null||typeof e!=\"object\")return [];let t=e;if(!Array.isArray(t.triplets))return [];let n=[];for(let o of t.triplets){if(o===null||typeof o!=\"object\")continue;let r=o;typeof r.sugar==\"string\"&&typeof r.base==\"string\"&&typeof r.linker==\"string\"&&n.push({sugar:r.sugar,base:r.base,linker:r.linker});}return n}_saveFavorites(){let e=this._localStorage();if(e!==null)try{let t={symbols:Array.from(this._favorites)};this._favoriteTriplets.length>0&&(t.triplets=this._favoriteTriplets.map(n=>({...n}))),e.setItem(Li,JSON.stringify(t));}catch{}}};qe._DEFAULT_TRIPLET_BASES=[\"A\",\"C\",\"G\",\"U\",\"T\"],qe._PALETTE_RDKIT_CACHE_LIMIT=256;var lt=qe;var U='<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.5\" stroke-linecap=\"round\" stroke-linejoin=\"round\">',Sa={new:`${U}<path d=\"M13 3H7a2 2 0 0 0-2 2v14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V9z\"/><path d=\"M13 3v6h6\"/><line x1=\"12\" y1=\"12.5\" x2=\"12\" y2=\"17.5\"/><line x1=\"9.5\" y1=\"15\" x2=\"14.5\" y2=\"15\"/></svg>`,open:`${U}<path d=\"m6 14 1.45-2.9A2 2 0 0 1 9.24 10H20a2 2 0 0 1 1.94 2.5l-1.55 6a2 2 0 0 1-1.94 1.5H4a2 2 0 0 1-2-2V5a2 2 0 0 1 2-2h3.93a2 2 0 0 1 1.66.9l.82 1.2a2 2 0 0 0 1.66.9H18a2 2 0 0 1 2 2v2\"/></svg>`,save:`${U}<rect x=\"8\" y=\"2\" width=\"8\" height=\"4\" rx=\"1\" ry=\"1\"/><path d=\"M16 4h2a2 2 0 0 1 2 2v14a2 2 0 0 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theme\"},Ri=[{id:\"new\",label:\"New\",icon:\"New\"},{id:\"open\",label:\"Open\",icon:\"Open\"},{id:\"save\",label:\"Save\",icon:\"Save\"},{id:\"undo\",label:\"Undo\",icon:\"\\u21BA\",shortcut:\"Ctrl+Z\",separator:true},{id:\"redo\",label:\"Redo\",icon:\"\\u21BB\",shortcut:\"Ctrl+Y\"},{id:\"eraser\",label:\"Eraser\",icon:\"Eraser\",separator:true},{id:\"select\",label:\"Select\",icon:\"Select\"},{id:\"hbond\",label:\"H-Bond\",icon:\"H-Bond\"},{id:\"zoom-in\",label:\"Zoom In\",icon:\"+\",shortcut:\"Ctrl++\",separator:true},{id:\"zoom-out\",label:\"Zoom Out\",icon:\"\\u2212\",shortcut:\"Ctrl+\\u2212\"},{id:\"fit\",label:\"Fit\",icon:\"Fit\",shortcut:\"0\"},{id:\"move\",label:\"Move\",icon:\"Move\"},{id:\"clean\",label:\"Clean\",icon:\"Clean\",separator:true},{id:\"find\",label:\"Find\",icon:\"Find\",shortcut:\"Ctrl+F\"},{id:\"theme\",label:\"Theme\",icon:\"Theme\",separator:true}],dt=class{constructor(e,t,n){this._buttons=new Map;this._unsubs=[];this._destroyed=false;this._editor=t,this._doc=n?.documentImpl??S(e);let o=n?.buttons??Ri;this.element=g(this._doc,\"div\",{class:\"hw-toolbar\",\"data-testid\":\"toolbar\"}),e.appendChild(this.element);for(let s of o){if(s.separator===true){let l=g(this._doc,\"span\",{class:\"hw-toolbar__separator\"});this.element.appendChild(l);}let a=this._buildButton(s);this.element.appendChild(a),this._buttons.set(s.id,a);}let r=()=>this._refreshHistoryState();this._unsubs.push(t.on(\"mol:changed\",r)),this._unsubs.push(t.on(\"helm:changed\",r)),r(),this._reflectMode(),this._unsubs.push(t.on(\"option:change\",s=>{s.key===\"mode\"&&this._reflectMode();}));}setButtonEnabled(e,t){let n=this._buttons.get(e);n!==void 0&&(t?n.removeAttribute(\"disabled\"):n.setAttribute(\"disabled\",\"\"));}destroy(){if(!this._destroyed){this._destroyed=true,this._hideTip();for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_buildButton(e){let t=this._doc.createElement(\"button\");t.setAttribute(\"class\",\"hw-toolbar__btn\"),t.setAttribute(\"type\",\"button\"),t.setAttribute(\"data-action\",e.id),t.setAttribute(\"data-testid\",`toolbar-${e.id}`);let n=Ea[e.id]??e.label,o=e.shortcut!==void 0?`${n}  (${e.shortcut})`:n;t.setAttribute(\"data-tooltip\",o),t.setAttribute(\"aria-label\",n),t.addEventListener(\"mouseenter\",s=>{let a=s;this._showTip(o,typeof a.clientX==\"number\"?a.clientX:0,typeof a.clientY==\"number\"?a.clientY:0);}),t.addEventListener(\"mouseleave\",()=>this._hideTip()),t.addEventListener(\"click\",()=>this._hideTip());let r=Sa[e.id];if(r!==void 0){let s=this._doc.createElement(\"span\");s.setAttribute(\"class\",\"hw-toolbar__btn-icon\"),s.setAttribute(\"aria-hidden\",\"true\"),s.innerHTML=r,t.appendChild(s);}else {let s=e.icon??e.label;t.appendChild(this._doc.createTextNode(s));}return t.addEventListener(\"click\",()=>this._invoke(e.id)),t}_showTip(e,t,n){let o=oe(this._doc,\"toolbar-tooltip\",\"hw-toolbar-tooltip\");for(;o.firstChild!==null;)o.removeChild(o.firstChild);o.appendChild(this._doc.createTextNode(e)),Y(o,t,n);}_hideTip(){V(this._doc.body.querySelector('[data-testid=\"toolbar-tooltip\"]'));}_invoke(e){let t=false;this._editor.fire(\"key:command\",{command:e,preventDefault:()=>{t=true;}}),!t&&this._execute(e);}_execute(e){switch(e){case \"new\":this._editor.setHelm(\"\");return;case \"open\":{let t=this._doc.defaultView;if(t!=null&&typeof t.prompt==\"function\"){let n=t.prompt(\"Enter HELM string\");n!==null&&this._editor.setHelm(n);}return}case \"save\":{let t=this._editor.getHelm();this._editor.fire(\"clipboard:copy\",{format:\"helm\",payload:t});return}case \"undo\":this._editor.undo();return;case \"redo\":this._editor.redo();return;case \"eraser\":{if(!this._editor.getSelection().isEmpty){this._editor.deleteSelection();return}this._editor.setMode(\"eraser\");return}case \"select\":case \"hbond\":case \"move\":this._editor.setMode(e);return;case \"zoom-in\":this._editor.zoom(1.1,this._molCenterOrUndefined());return;case \"zoom-out\":this._editor.zoom(1/1.1,this._molCenterOrUndefined());return;case \"fit\":this._editor.fitToContent();return;case \"clean\":this._editor.cleanLayout();return;case \"find\":this._editor.openFindReplace();return;case \"theme\":{let t=this._editor,n=typeof t._currentTheme==\"function\"?t._currentTheme():null,o=n!==null&&n.name===\"dark\";this._editor.setTheme(o?H:En);return}default:return}}_refreshHistoryState(){this.setButtonEnabled(\"undo\",this._editor.canUndo()),this.setButtonEnabled(\"redo\",this._editor.canRedo());}_molCenterOrUndefined(){let e=this._editor.getMol();if(e.atoms.length===0)return;let t=e.atoms[0].p.x,n=t,o=e.atoms[0].p.y,r=o;for(let s=1;s<e.atoms.length;s++){let a=e.atoms[s].p;a.x<t&&(t=a.x),a.x>n&&(n=a.x),a.y<o&&(o=a.y),a.y>r&&(r=a.y);}return {x:(t+n)/2,y:(o+r)/2}}_reflectMode(){let e=this._editor.getMode();for(let t of [\"select\",\"eraser\",\"hbond\",\"move\"]){let n=this._buttons.get(t);if(n===void 0)continue;let r=(n.getAttribute(\"class\")??\"\").split(/\\s+/).filter(s=>s!==\"hw-toolbar__btn--active\").join(\" \");n.setAttribute(\"class\",t===e?`${r} hw-toolbar__btn--active`:r);}}};var ct=class{constructor(e,t,n){this._unsubs=[];this._destroyed=false;this._editor=t,this._doc=n?.documentImpl??S(e),this._content=g(this._doc,\"pre\",{class:\"hw-pane__content hw-pane__sequence\",\"data-testid\":\"sequence-pane-content\"}),this.element=g(this._doc,\"div\",{class:\"hw-pane hw-pane--sequence\",\"data-testid\":\"pane-sequence\"},[this._content]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on(\"helm:changed\",()=>this.refresh())),this._unsubs.push(t.on(\"mol:changed\",()=>this.refresh()));}refresh(){if(this._destroyed)return;let e=this._compute();for(;this._content.firstChild!==null;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e));}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_compute(){let e=this._editor.getMol(),t=[],n;for(let o of e.atoms){let r=o.bio.chainId;n!==void 0&&r!==n&&t.push(\"|\"),n=r;let s=o.monomer?.naturalAnalog;t.push(s!==void 0&&s!==\"\"?s:o.symbol);}return t.join(\"\")}};var ut=class{constructor(e,t,n){this._unsubs=[];this._destroyed=false;this._suppressNext=false;this._editor=t,this._doc=n?.documentImpl??S(e),this._input=g(this._doc,\"div\",{class:\"hw-pane__content hw-pane__notation\",contenteditable:\"true\",spellcheck:\"false\",\"data-testid\":\"notation-pane-content\"}),this._error=g(this._doc,\"div\",{class:\"hw-pane__error\",\"data-testid\":\"notation-pane-error\"}),this.element=g(this._doc,\"div\",{class:\"hw-pane hw-pane--notation\",\"data-testid\":\"pane-helm\"},[this._input,this._error]),e.appendChild(this.element),this.refresh(),this._input.addEventListener(\"blur\",()=>this._commit()),this._input.addEventListener(\"keydown\",o=>{o.key===\"Enter\"&&(o.preventDefault(),o.stopPropagation(),o.stopImmediatePropagation(),this._commit());}),this._unsubs.push(t.on(\"helm:changed\",()=>{if(this._suppressNext){this._suppressNext=false;return}this.refresh();})),this._unsubs.push(t.on(\"mol:changed\",()=>this.refresh()));}refresh(){if(this._destroyed)return;let e=this._editor.getHelm();for(;this._input.firstChild!==null;)this._input.removeChild(this._input.firstChild);this._input.appendChild(this._doc.createTextNode(e)),this._clearError();}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_commit(){if(this._destroyed)return;let e=(this._input.textContent??\"\").trim(),t=this._editor.getHelm();if(e===t){this._clearError();return}let r=this._editor.getService().validate(e).filter(s=>s.severity===\"error\");if(r.length>0){this._showError(r.map(s=>s.message).join(\"; \"));return}this._clearError(),this._suppressNext=true,this._editor.setHelm(e);}_showError(e){for(;this._error.firstChild!==null;)this._error.removeChild(this._error.firstChild);this._error.appendChild(this._doc.createTextNode(e)),this._error.setAttribute(\"class\",\"hw-pane__error hw-pane__error--visible\");}_clearError(){for(;this._error.firstChild!==null;)this._error.removeChild(this._error.firstChild);this._error.setAttribute(\"class\",\"hw-pane__error\");}};var Ca=1e3,mt=class{constructor(e,t,n){this._unsubs=[];this._destroyed=false;this._editor=t,this._doc=n?.documentImpl??S(e),this._body=g(this._doc,\"div\",{class:\"hw-pane__content hw-pane__properties\",\"data-testid\":\"properties-pane-content\"}),this.element=g(this._doc,\"div\",{class:\"hw-pane hw-pane--properties\",\"data-testid\":\"pane-properties\"},[this._body]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on(\"helm:changed\",()=>this.refresh())),this._unsubs.push(t.on(\"mol:changed\",()=>this.refresh()));}refresh(){if(this._destroyed)return;for(;this._body.firstChild!==null;)this._body.removeChild(this._body.firstChild);let e=this._editor.getHelm();if(e.length>Ca){this._body.appendChild(g(this._doc,\"div\",{class:\"hw-pane__placeholder\"},[\"(too long)\"]));return}let t=this._editor.getService(),n=\"\",o=0,r=0;try{let s=t.getFormula(e);n=La(s.elements),o=s.mw;}catch{n=\"\\u2014\";}try{o=t.getMolWeight(e);}catch{}try{r=t.getExtinctionCoefficient(e);}catch{}this._body.appendChild(this._makeRow(\"Formula\",n,\"formula\")),this._body.appendChild(this._makeRow(\"Molecular Weight\",o===0?\"\\u2014\":o.toFixed(2),\"mw\")),this._body.appendChild(this._makeRow(\"Extinction Coefficient\",r===0?\"\\u2014\":r.toFixed(0),\"extinction\"));}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_makeRow(e,t,n){let o=g(this._doc,\"span\",{class:\"hw-pane__prop-label\"},[e]),r=g(this._doc,\"span\",{class:\"hw-pane__prop-value\",\"data-testid\":`properties-${n}`},[t]);return g(this._doc,\"div\",{class:\"hw-pane__prop-row\"},[o,r])}};function La(i){let e=Array.from(i.keys()).sort((n,o)=>n===o?0:n===\"C\"?-1:o===\"C\"?1:n===\"H\"?-1:o===\"H\"?1:n.localeCompare(o)),t=\"\";for(let n of e){let o=i.get(n);o===void 0||o===0||(t+=o===1?n:`${n}${o}`);}return t===\"\"?\"\\u2014\":t}var pt=class{constructor(e,t,n){this._unsubs=[];this._destroyed=false;this._refreshToken=0;this._editor=t,this._doc=n?.documentImpl??S(e),this._content=g(this._doc,\"pre\",{class:\"hw-pane__content hw-pane__atomic\",\"data-testid\":\"atomic-pane-content\"}),this.element=g(this._doc,\"div\",{class:\"hw-pane hw-pane--atomic\",\"data-testid\":\"pane-atomic\"},[this._content]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on(\"helm:changed\",()=>{this.refresh();}));}async refresh(){if(this._destroyed)return;let e=++this._refreshToken,t=this._editor.getHelm(),n=this._editor.getService();if(!n.hasAtomicMolfileProvider()){this._render(\"Atomic structure unavailable\");return}try{let o=await n.getAtomicMolfile(t);if(this._destroyed||e!==this._refreshToken)return;this._render(o);}catch(o){if(this._destroyed||e!==this._refreshToken)return;let r=o instanceof Error?o.message:String(o);this._render(`Atomic structure unavailable: ${r}`);}}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_render(e){for(;this._content.firstChild!==null;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e));}};function Yt(i){return i.toLowerCase().replace(/[^a-z0-9]+/g,\"-\").replace(/^-|-$/g,\"\")}var ht=class{constructor(e,t,n,o,r){this._unsubs=[];this._destroyed=false;this._active=false;this._dirty=true;this._refreshToken=0;this._editor=t,this._provider=o,this.name=n,this._doc=r?.documentImpl??S(e);let s=Yt(n);this._content=g(this._doc,\"div\",{class:\"hw-pane__content hw-pane__extra\",\"data-testid\":`extra-pane-content-${s}`}),this.element=g(this._doc,\"div\",{class:\"hw-pane hw-pane--extra\",\"data-testid\":`pane-extra-${s}`},[this._content]),e.appendChild(this.element),this._unsubs.push(t.on(\"helm:changed\",()=>{this._dirty=true,this._active&&this.refresh();}));}setActive(e){this._active=e,e&&this._dirty&&this.refresh();}async refresh(){if(this._destroyed)return;let e=++this._refreshToken;this._dirty=false;let t=this._editor.getHelm();try{let n=await this._provider(t);if(this._destroyed||e!==this._refreshToken)return;this._mount(n);}catch(n){if(this._destroyed||e!==this._refreshToken)return;let o=n instanceof Error?n.message:String(n);this._renderText(`Pane \"${this.name}\" failed: ${o}`);}}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_mount(e){for(;this._content.firstChild!==null;)this._content.removeChild(this._content.firstChild);this._content.appendChild(e);}_renderText(e){for(;this._content.firstChild!==null;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e));}};var Ba=\"extra:\";function Xt(i){return Ba+i}var Ra=[{id:\"sequence\",label:\"Sequence\"},{id:\"helm\",label:\"HELM\"},{id:\"properties\",label:\"Properties\"},{id:\"atomic\",label:\"Atomic Structure\"}],ft=class{constructor(e,t){this._paneByName=new Map;this._tabsByName=new Map;this._unsubs=[];this._activePane=\"helm\";this._destroyed=false;this._statusModeNode=null;this._statusMessageNode=null;this._statusMessageTimeout=null;this._host=e,this._doc=t.documentImpl??S(e);let o=(t.theme??H).name===\"dark\"?\"hw-app hw-app--dark\":\"hw-app\";this.element=g(this._doc,\"div\",{class:o,\"data-testid\":\"app-root\"}),this._toolbarHost=g(this._doc,\"div\",{class:\"hw-app__toolbar\"}),this._paletteHost=g(this._doc,\"div\",{class:\"hw-app__palette\"}),this._canvasHost=g(this._doc,\"div\",{class:\"hw-app__canvas\",\"data-testid\":\"canvas-host\"});let r=g(this._doc,\"div\",{class:\"hw-app__main\"},[this._paletteHost,this._canvasHost]);this._tabsHost=g(this._doc,\"div\",{class:\"hw-app__tabs\",role:\"tablist\"}),this._paneBody=g(this._doc,\"div\",{class:\"hw-app__pane-body\"});let s=g(this._doc,\"div\",{class:\"hw-app__panes\"},[this._tabsHost,this._paneBody]);this.element.appendChild(this._toolbarHost),this.element.appendChild(r),this.element.appendChild(s),e.appendChild(this.element);let a={service:t.service};t.initialHelm!==void 0&&(a.initialHelm=t.initialHelm),t.width!==void 0&&(a.width=t.width),t.height!==void 0&&(a.height=t.height),this.canvas=new rt(this._canvasHost,a),t.theme!==void 0&&this.canvas.setTheme(t.theme);let l={documentImpl:this._doc};t.toolbarButtons!==void 0&&(l.buttons=t.toolbarButtons),this.toolbar=new dt(this._toolbarHost,this.canvas,l),this.palette=new lt(this._paletteHost,this.canvas,{documentImpl:this._doc,...t.paletteOptions}),this.sequencePane=new ct(this._paneBody,this.canvas,{documentImpl:this._doc}),this.notationPane=new ut(this._paneBody,this.canvas,{documentImpl:this._doc}),this.propertiesPane=new mt(this._paneBody,this.canvas,{documentImpl:this._doc}),t.service.hasAtomicMolfileProvider()?this.atomicStructurePane=new pt(this._paneBody,this.canvas,{documentImpl:this._doc}):this.atomicStructurePane=null,this._paneByName.set(\"sequence\",this.sequencePane.element),this._paneByName.set(\"helm\",this.notationPane.element),this._paneByName.set(\"properties\",this.propertiesPane.element),this.atomicStructurePane!==null&&this._paneByName.set(\"atomic\",this.atomicStructurePane.element);let d=[];for(let[p,h]of t.service.getExtraPanes()){let f=new ht(this._paneBody,this.canvas,p,h,{documentImpl:this._doc});d.push(f),this._paneByName.set(Xt(p),f.element);}this.extraPanes=d;let c=this._resolveVisiblePanes(t),u=[];for(let p of c){let h=Ra.find(f=>f.id===p);h!==void 0&&u.push({id:h.id,label:h.label,testid:`tab-${h.id}`});}for(let p of d)u.push({id:Xt(p.name),label:p.name,testid:`tab-extra-${Yt(p.name)}`});for(let{id:p,label:h,testid:f}of u){let y=this._doc.createElement(\"button\");y.setAttribute(\"type\",\"button\"),y.setAttribute(\"class\",\"hw-app__tab\"),y.setAttribute(\"role\",\"tab\"),y.setAttribute(\"data-pane\",p),y.setAttribute(\"data-testid\",f),y.appendChild(this._doc.createTextNode(h)),y.addEventListener(\"click\",()=>this.activatePane(p)),this._tabsHost.appendChild(y),this._tabsByName.set(p,y);}let m=c.includes(\"helm\")?\"helm\":c[0]??\"helm\";this.activatePane(m),this._unsubs.push(this.canvas.on(\"theme:change\",p=>this._applyTheme(p.theme))),this._buildStatusBar(),this._applyMode(this.canvas.getMode()),this._unsubs.push(this.canvas.on(\"option:change\",p=>{p.key===\"mode\"&&this._applyMode(p.newValue),p.key===\"nextAdd\"&&this._refreshStatus();})),this._unsubs.push(this.canvas.on(\"mol:changed\",()=>this._refreshStatus())),this._unsubs.push(this.canvas.on(\"helm:changed\",()=>this._refreshStatus())),this._unsubs.push(this.canvas.on(\"editor:status\",p=>{this._showStatusMessage(p.message,p.severity,p.durationMs);})),this._unsubs.push(this.canvas.on(\"monomer:contextmenu\",p=>{p.preventDefault(),this.canvas.openAtomProps(p.atom);})),this._unsubs.push(this.canvas.on(\"bond:contextmenu\",p=>{p.preventDefault(),this.canvas.openBondProps(p.bond);})),this._onDocKeydown=p=>this._handleEscape(p),this._doc.addEventListener(\"keydown\",this._onDocKeydown,true);}_handleEscape(e){let t=e;t.key===\"Escape\"&&(Ot(this._doc),X.closeTopmost()&&(t.stopImmediatePropagation?.(),t.preventDefault?.()));}_buildStatusBar(){let e=g(this._doc,\"div\",{class:\"hw-status-bar\",\"data-testid\":\"status-bar\"}),t=g(this._doc,\"span\",{class:\"hw-status-bar__mode\",\"data-testid\":\"status-mode\"}),n=g(this._doc,\"span\",{class:\"hw-status-bar__message\",\"data-testid\":\"status-message\",role:\"status\",\"aria-live\":\"polite\"});e.appendChild(t),e.appendChild(n),this._canvasHost.appendChild(e),this._statusModeNode=t,this._statusMessageNode=n,this._refreshStatus();}_refreshStatus(){let e=this._statusModeNode;if(e===null)return;let t=this.canvas.getMode(),n=this.canvas.getNextAddSymbol();for(;e.firstChild!==null;)e.removeChild(e.firstChild);if(n===null){e.appendChild(this._doc.createTextNode(`Mode: ${t}  |  Next add: none`));return}e.appendChild(this._doc.createTextNode(`Mode: ${t}  |  Next add: `));let o=g(this._doc,\"span\",{class:\"hw-status-bar__next-add-symbol\",\"data-testid\":\"status-next-add-symbol\"},[n.symbol]);e.appendChild(o);let r=g(this._doc,\"button\",{type:\"button\",class:\"hw-status-bar__next-add-clear\",\"data-testid\":\"status-next-add-clear\",\"aria-label\":\"Clear next-add monomer\",title:\"Clear (Esc)\"},[\"\\xD7\"]);r.addEventListener(\"click\",s=>{s.preventDefault(),s.stopPropagation(),this.canvas.setNextAddSymbol(null);}),e.appendChild(r);}_showStatusMessage(e,t,n){let o=this._statusMessageNode;if(o!==null){for(this._statusMessageTimeout!==null&&(clearTimeout(this._statusMessageTimeout),this._statusMessageTimeout=null);o.firstChild!==null;)o.removeChild(o.firstChild);o.appendChild(this._doc.createTextNode(e)),o.setAttribute(\"data-severity\",t),n>0&&(this._statusMessageTimeout=setTimeout(()=>{let r=this._statusMessageNode;if(r!==null){for(;r.firstChild!==null;)r.removeChild(r.firstChild);r.removeAttribute(\"data-severity\"),this._statusMessageTimeout=null;}},n));}}_applyMode(e){let t=this._canvasHost.querySelector(\".hw-editor-view\");if(t===null)return;let o=(t.getAttribute(\"class\")??\"\").split(/\\s+/).filter(r=>!r.startsWith(\"hw-editor-view--\")).join(\" \");t.setAttribute(\"class\",`${o} hw-editor-view--${e}`.trim()),this._refreshStatus();}setHelm(e){this.canvas.setHelm(e);}getHelm(){return this.canvas.getHelm()}on(e,t){return this.canvas.on(e,t)}activatePane(e){if(!(!this._paneByName.has(e)&&!this._tabsByName.has(e))){this._activePane=e;for(let[t,n]of this._paneByName.entries())n.style.display=t===e?\"\":\"none\";for(let[t,n]of this._tabsByName.entries()){let r=(n.getAttribute(\"class\")??\"\").split(/\\s+/).filter(s=>s!==\"hw-app__tab--active\").join(\" \");n.setAttribute(\"class\",t===e?`${r} hw-app__tab--active`:r);}for(let t of this.extraPanes)t.setActive(this._activePane===Xt(t.name));}}getActivePane(){return this._activePane}destroy(){if(!this._destroyed){this._destroyed=true,this._statusMessageTimeout!==null&&(clearTimeout(this._statusMessageTimeout),this._statusMessageTimeout=null),this._doc.removeEventListener(\"keydown\",this._onDocKeydown,true);for(let e of this._unsubs)e();for(let e of this.extraPanes)e.destroy();this.atomicStructurePane!==null&&this.atomicStructurePane.destroy(),this.propertiesPane.destroy(),this.notationPane.destroy(),this.sequencePane.destroy(),this.palette.destroy(),this.toolbar.destroy(),this.canvas.destroy(),this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element),this._host;}}_resolveVisiblePanes(e){let t=e.service.hasAtomicMolfileProvider(),n=e.visiblePanes??[\"sequence\",\"helm\",\"properties\",\"atomic\"];return t||(n=n.filter(o=>o!==\"atomic\")),n}_applyTheme(e){let t=e.name===\"dark\",o=(this.element.getAttribute(\"class\")??\"\").split(/\\s+/).filter(r=>r!==\"hw-app--dark\").join(\" \");this.element.setAttribute(\"class\",t?`${o} hw-app--dark`:o);}};var Vn=class{constructor(e){this.T=\"ATOM\";this.selected=e.selected,this.highlighted=e.highlighted,this.p={x:e.p.x,y:e.p.y},this.elem=e.symbol,this.bio={type:e.biotype,continuousId:e.bio.continuousId,chainId:e.bio.chainId,positionInChain:e.bio.positionInChain,...e.bio.annotation!==void 0?{annotation:e.bio.annotation}:{},...e.bio.blobtype!==void 0?{blobtype:e.bio.blobtype}:{},...e.bio.ambiguity!==void 0?{ambiguity:e.bio.ambiguity}:{},id:e.id},e.inlineSource!==void 0&&(this.inlineSource=e.inlineSource);}biotype(){return this.bio.type}},Un=class{constructor(e,t,n){this.a1=t,this.a2=n,this.r1=Ii(e.r1),this.r2=Ii(e.r2),this.kind=e.kind;}};function Ii(i){switch(i.kind){case \"numeric\":return i.r;case \"positional\":return i.r;default:return 0}}function re(i){let e=[],t=new Map;for(let r of i.atoms){let s=new Vn(r);e.push(s),t.set(r.id,s);}let n=[];for(let r of i.bonds){let s=t.get(r.a1.id),a=t.get(r.a2.id);s===void 0||a===void 0||n.push(new Un(r,s,a));}return {atoms:e,bonds:n,clone(r){return re(i)},_internalMol:i}}var Ia=400,Pa=100,Ha=14,se=class{constructor(e,t,n){this._laidMol=null;this._currentHelm=\"\";this._drawOptions={fontsize:Ha};this._noDraw=false;this._svgEl=null;this.host=e,this._service=t,this._doc=n?.documentImpl??S(e),this._width=n?.width??Ia,this._height=n?.height??Pa,this._mol=me(),this._molView=re(this._mol),this.editor=this._buildEditor();}resizeEditor(e,t){this._width=e,this._height=t,this._redraw();}_buildEditor(){let e=this,t={get noDraw(){return e._noDraw},set noDraw(n){e._noDraw=n;},get jsd(){return e.editor}};return {get div(){return e.host},get m(){return e._molView},set m(n){e._molView=n;},get helm(){return t},get options(){return {width:e._width,height:e._height}},setData(n,o){if(o!==\"helm\")throw new Error(`LegacyEditorWrapper: only 'helm' format supported (got '${o}').`);e._setHelm(n);},setHelm(n){e._setHelm(n);},setMol(n){e._mol=n._internalMol,e._molView=e._buildView(e._mol),e._currentHelm=e._service.serialize(e._mol),e._redraw();},getHelm(n){return e._currentHelm},getMolfile(){return Pt(e._mol)},resize(n,o){e._width=n,e._height=o,e._redraw();},setSize(n,o){e._width=n,e._height=o,e._redraw();},redraw(){e._redraw();},reset(){e._mol=me(),e._laidMol=null,e._molView=re(e._mol),e._currentHelm=\"\",e._removeSvg();},getFormula(n){return $a(fe(e._mol))},getMolWeight(){return Pe(e._mol)},getExtinctionCoefficient(){return He(e._mol)},getDrawOptions(){return e._drawOptions}}}_setHelm(e){this._currentHelm=e;let t=this._service.parse(e,{mode:\"lenient\",resolveMonomers:true});this._mol=t.mol,this._molView=this._buildView(this._mol),this._redraw();}_buildView(e){return this._laidMol=this._noDraw?null:ne(e),re(this._laidMol??e)}_redraw(){if(this._noDraw){this._removeSvg();return}if(this._currentHelm===\"\"||this._laidMol===null){this._removeSvg();return}let e=new Set,t=new Set;for(let o of this._molView.atoms){let r=o.bio.id;r!==void 0&&(o.selected&&e.add(r),o.highlighted&&t.add(r));}let n=this._service.renderMolResult(this._laidMol,{width:this._width,height:this._height,maxScale:1/0,showIds:true,selectedAtomIds:e,highlightedAtomIds:t});this._bakeViewToSurface(n.bbox,n.drawBox),this._mountSvg(n.svg);}_bakeViewToSurface(e,t){if(this._laidMol===null)return;let n=t.scale,o=t.x-e.x*n,r=t.y-e.y*n,s=this._laidMol.atoms,a=this._molView.atoms,l=Math.min(s.length,a.length);for(let d=0;d<l;d++){let c=s[d].p,u=a[d].p;u.x=c.x*n+o,u.y=c.y*n+r;}}_mountSvg(e){this._removeSvg();let t=Da(this._doc,e,this._width,this._height);t.setAttribute(\"pointer-events\",\"none\"),this.host.firstChild!==null?this.host.insertBefore(t,this.host.firstChild):this.host.appendChild(t),this._svgEl=t;}_removeSvg(){this._svgEl!==null&&this._svgEl.parentNode!==null&&this._svgEl.parentNode.removeChild(this._svgEl),this._svgEl=null;}},Pi=[\"C\",\"H\",\"N\",\"O\",\"S\",\"P\"];function $a(i){let e=o=>{let r=Pi.indexOf(o);return r===-1?Pi.length:r},t=[...i.elements.keys()].sort((o,r)=>{let s=e(o),a=e(r);return s!==a?s-a:o<r?-1:o>r?1:0}),n=[];for(let o of t){let r=i.elements.get(o);n.push(r===1?o:`${o}${r}`);}return n.join(\"\")}function Da(i,e,t,n){let o=Oa(i,e);if(o!==null)return o;let r=i.createElementNS(\"http://www.w3.org/2000/svg\",\"svg\");return r.setAttribute(\"width\",String(t)),r.setAttribute(\"height\",String(n)),r}function Oa(i,e){let t=globalThis.DOMParser;if(t===void 0)return null;try{let r=new t().parseFromString(e,\"image/svg+xml\").documentElement;return r==null?null:i.importNode(r,!0)}catch{return null}}var Na=800,Fa=400,Ga=32,Va=14,zn=class{constructor(e){this._width=0;this._height=0;this._doc=e;}resize(e,t){this._width=e,this._height=t;}select(){}dblclick(){}createMonomerDiv(e,t,n){let o=g(this._doc,\"div\",{\"data-monomer\":t,\"data-biotype\":n,\"data-testid\":`legacy-mex-monomer-${t}`});return e.appendChild(o),o}getSize(){return {width:this._width,height:this._height}}},bt=class{constructor(e,t,n){this.toolbarheight=Ga;this._drawOptions={fontsize:Va};this._unsubs=[];this._destroyed=false;this._host=e,this._service=t,this._doc=n?.documentImpl??S(e),this._width=n?.width??Na,this._height=n?.height??Fa;let o={service:t};n?.initialHelm!==void 0&&(o.initialHelm=n.initialHelm),n?.documentImpl!==void 0&&(o.documentImpl=n.documentImpl),n?.width!==void 0&&(o.width=n.width),n?.height!==void 0&&(o.height=n.height),this._app=new ft(e,o),this.sequence=this._app.sequencePane.element,this.notation=this._app.notationPane.element,this.properties={parent:this._app.propertiesPane.element},this._structureviewHost=g(this._doc,\"div\",{class:\"hwe-legacy-app__structureview\",\"data-testid\":\"legacy-app-structureview\"}),this._structureviewWrapper=new se(this._structureviewHost,t,{documentImpl:this._doc}),this.structureview=this._structureviewWrapper,this.mex=new zn(this._doc),this._editorFacade=this._buildEditorFacade();let r=this._editorFacade;this.canvas={get host(){return r.div},get editor(){return r},get helm(){return r.helm},resizeEditor:(a,l)=>{this._resize(a,l);},getHelm:a=>r.getHelm(a),setHelm:a=>{r.setHelm(a);}};let s=()=>{this._structureviewWrapper.editor.setHelm(this._app.getHelm());};this._unsubs.push(this._app.canvas.on(\"helm:changed\",s)),n?.initialHelm!==void 0&&n.initialHelm.length>0&&s();}get editorApp(){return this._app}_buildEditorFacade(){let e=this,t=this._app,n={noDraw:false,get jsd(){return e._editorFacade}};return {get div(){return t.element},get m(){return e._currentMolView()},set m(o){o!=null&&o._internalMol!==void 0&&t.canvas.setMol(o._internalMol);},get helm(){return n},get options(){return {width:e._width,height:e._height}},setData(o,r){if(r!==\"helm\")throw new Error(`LegacyAppWrapper: only 'helm' format supported (got '${r}').`);t.setHelm(o);},setHelm(o){t.setHelm(o);},setMol(o){t.canvas.setMol(o._internalMol);},getHelm(o){return t.getHelm()},getMolfile(){return e._service.getMolfile(t.getHelm())},resize(o,r){e._resize(o,r);},setSize(o,r){e._resize(o,r);},redraw(){t.canvas.redraw();},reset(){t.setHelm(\"\");},getFormula(o){return Ua(fe(t.canvas.getMol()))},getMolWeight(){return Pe(t.canvas.getMol())},getExtinctionCoefficient(){return He(t.canvas.getMol())},getDrawOptions(){return e._drawOptions}}}_currentMolView(){let e=this._app.canvas.getMol(),t=re(e),n=this._app.canvas.getSelection();if(!n.isEmpty)for(let o of t.atoms){let r=o.bio.id;typeof 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