@datagrok/helm 3.0.1 → 3.0.2

package/dist/package-test.js

@@ -1,2 +1,2 @@
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gt{constructor(t,e,i){this.name=t,this.alphabet=e,this.cutoff=i}}!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(ut||(ut={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(pt||(pt={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions",t.positionShift=".positionShift",t.selectedPosition=".selectedPosition",t.polymerTypeColumnName=".polymerTypeColumnName",t.annotations=".annotations",t.numberingScheme=".numberingScheme",t.annotationColumnName=".annotationColumnName"}(ft||(ft={}));const mt=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};new 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o=ke(i,n,220,140);if(this._rdkitSvgCache.size>=t._RDKIT_CACHE_LIMIT){let t=this._rdkitSvgCache.keys().next().value;void 0!==t&&this._rdkitSvgCache.delete(t)}return this._rdkitSvgCache.set(r,o),o}_hideTooltip(){Me(this._tooltip)}_showBondTooltip(t,e,i){let s=this._bondTooltip;if(null===s)return;let n=Oe(t.r1),r=Oe(t.r2),o=`${t.a1.symbol}@${t.a1.bio.chainId}:${t.a1.bio.positionInChain}`,l=`${t.a2.symbol}@${t.a2.bio.chainId}:${t.a2.bio.positionInChain}`;$e(this._doc,s,{symbol:`${n}-${r} (${t.kind})`,name:`${o} ↔ ${l}`}),Ie(s,e,i)}_hideBondTooltip(){Me(this._bondTooltip)}_paintBondPreview(t,e,i){let s=this._svgRoot.querySelector(".hw-content");if(null===s)return;let n=s.querySelector(".hw-bond-preview");null===n&&(n=this._doc.createElementNS("http://www.w3.org/2000/svg","line"),n.setAttribute("class","hw-bond-preview"),n.setAttribute("data-testid","bond-preview"),n.setAttribute("stroke-dasharray","6 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r=n.querySelector(".hw-selection-rect");null===r&&(r=this._doc.createElementNS("http://www.w3.org/2000/svg","rect"),r.setAttribute("class","hw-selection-rect"),r.setAttribute("data-testid","selection-rect"),r.setAttribute("fill","rgba(31, 95, 205, 0.08)"),r.setAttribute("stroke","#1f5fcd"),r.setAttribute("stroke-width","1"),r.setAttribute("stroke-dasharray","4 3"),r.setAttribute("pointer-events","none"),n.appendChild(r)),r.setAttribute("x",String(t)),r.setAttribute("y",String(e)),r.setAttribute("width",String(i)),r.setAttribute("height",String(s))}_clearSelectionRect(){let t=this._svgRoot.querySelector(".hw-selection-rect");null!==t&&null!==t.parentNode&&t.parentNode.removeChild(t)}};Le._RDKIT_CACHE_LIMIT=256;function Oe(t){switch(t.kind){case"numeric":return`R${t.r}`;case"unspecified":return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${t.position}pos:R${t.r}`}}var Re=class t{constructor(t,e){this._onClose=null,this._primaryAction=null,this._host=t,this._doc=e.documentImpl??Ee(t);let i=this._doc,s={class:"hw-modal-backdrop",role:"presentation"};void 0!==e.testId&&(s["data-testid"]=`dialog-${e.testId}`);let n=Pe(i,"div",s),r={class:"hw-modal",role:"dialog","aria-modal":"true","aria-label":e.title};void 0!==e.testId&&(r["data-testid"]=`dialog-${e.testId}-frame`);let o=Pe(i,"div",r),l=Pe(i,"div",{class:"hw-modal__header"},[e.title]),a=Pe(i,"div",{class:"hw-modal__body"});o.appendChild(l),o.appendChild(a),n.appendChild(o);let c=t=>{t.stopPropagation()};for(let t of["mousedown","mousemove","mouseup","mouseover","mouseenter","mouseleave","wheel","contextmenu","dblclick","keydown","keyup","keypress"])n.addEventListener(t,c);o.addEventListener("keydown",t=>{let e=t;if("Enter"!==e.key||"TEXTAREA"===e.target?.tagName)return;let i=this._primaryAction;null!==i&&(e.preventDefault?.(),e.stopImmediatePropagation?.(),i())}),n.addEventListener("click",t=>{t.target!==n?t.stopPropagation():this.close()}),this.root=n,this.body=a}static anyOpen(){return t._openStack.length>0}static closeTopmost(){let e=t._openStack[t._openStack.length-1];return void 0!==e&&(e.close(),!0)}open(e){this._onClose=e??null,null===this.root.parentNode&&this._host.appendChild(this.root),t._openStack.includes(this)||t._openStack.push(this),Ne(this._doc)}close(){let e=t._openStack.indexOf(this);e>=0&&t._openStack.splice(e,1),null!==this.root.parentNode&&this.root.parentNode.removeChild(this.root);let i=this._onClose;this._onClose=null,null!==i&&i()}setPrimaryAction(t){this._primaryAction=t}get isOpen(){return null!==this.root.parentNode}};Re._openStack=[];Object.freeze(new Set);function Fe(t){return t.startsWith("[")&&t.endsWith("]")||1===t.length&&/^[A-Za-z]$/.test(t)?t:`[${t}]`}function De(t,e,i){return`${Fe(t)}(${Fe(e)})${Fe(i)}`}var He="http://www.w3.org/2000/svg",Be={sugar:At,base:Et,linker:Pt},Ge={sugar:["r","R"],base:["A"],linker:["p","P"]},Ve={x:70,y:60},Ue={x:140,y:60},We={x:70,y:130},Ye=class t{constructor(t,e,i){this.onValueSet=new Mt,this.onPickModeChange=new Mt,this._slots=new Map,this._favStar=null,this._pickMode=null,this._destroyed=!1,this._builderRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??Ee(t),this._hooks=i?.paletteHooks??null,this._favHooks=i?.favoriteHooks??null,this.element=Pe(this._doc,"div",{class:"hw-rna-builder","data-testid":"rna-builder"});let s=Pe(this._doc,"div",{class:"hw-rna-builder__header"});if(s.appendChild(Pe(this._doc,"div",{class:"hw-rna-builder__title"},["RNA builder"])),null!==this._favHooks){let t=Pe(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"},["☆"]),e=t=>{t.stopPropagation();let e=this.getSelection();""===e.preview||null===this._favHooks||this._favHooks.toggleFavoriteTriplet(e.sugar,e.base,e.linker)};t.addEventListener("click",e),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&e(t)}),this._favStar=t,s.appendChild(t)}this.element.appendChild(s),this._hintEl=Pe(this._doc,"div",{class:"hw-rna-builder__hint","data-testid":"rna-builder-hint",hidden:!0}),this.element.appendChild(this._hintEl);let n=this._buildSvg();this.element.appendChild(n),this._preview=Pe(this._doc,"div",{class:"hw-rna-builder__preview","data-testid":"rna-builder-preview"}),this.element.appendChild(this._preview),this._addBtn=Pe(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),t.appendChild(this.element);let r=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),o=e.on("theme:change",()=>{this._destroyed||this._repaintSlotColors()});this._libUnsub=()=>{try{r()}catch{}try{o()}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}getSelection(){let t=this._slots.get("sugar")?.value??"",e=this._slots.get("base")?.value??"",i=this._slots.get("linker")?.value??"";return{sugar:t,base:e,linker:i,preview:""!==t&&""!==e&&""!==i?De(t,e,i):""}}setField(t,e){let i=this._slots.get(t);void 0!==i&&(i.value=e,this._setLabelText(i.labelEl,e),this._repaintSlot(i),this._updatePreview(),this.onValueSet.next({field:t,symbol:e}))}startPickMode(t){this._pickMode!==t?(null!==this._pickMode&&this._setSlotPressed(this._pickMode,!1),this._pickMode=t,this._setSlotPressed(t,!0),this._setHintActive(t),this.onPickModeChange.next({field:t}),null!==this._hooks&&this._hooks.beginBiotypeFilter(Be[t],e=>{this.setField(t,e),this._exitPickMode()},()=>{this._exitPickMode()})):this.cancelPickMode()}cancelPickMode(){null!==this._pickMode&&(null!==this._hooks&&this._hooks.endBiotypeFilter(),this._exitPickMode())}getPickMode(){return this._pickMode}triggerAdd(){this._onAddClicked()}destroy(){this._destroyed||(this._destroyed=!0,null!==this._pickMode&&null!==this._hooks&&this._hooks.endBiotypeFilter(),this._libUnsub(),this.onValueSet.complete(),this.onPickModeChange.complete(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}_buildSvg(){let t=this._doc.createElementNS(He,"svg");t.setAttribute("class","hw-rna-builder__triplet"),t.setAttribute("viewBox","0 0 200 180"),t.setAttribute("data-testid","rna-builder-triplet-svg"),t.setAttribute("role","group"),t.setAttribute("aria-label","Triplet preview");let e=this._doc.createElementNS(He,"line");e.setAttribute("class","hw-rna-builder__bond"),e.setAttribute("x1",String(Ve.x+18)),e.setAttribute("y1",String(Ve.y)),e.setAttribute("x2",String(Ue.x-18)),e.setAttribute("y2",String(Ue.y)),t.appendChild(e);let i=this._doc.createElementNS(He,"line");i.setAttribute("class","hw-rna-builder__bond"),i.setAttribute("x1",String(Ve.x)),i.setAttribute("y1",String(Ve.y+18)),i.setAttribute("x2",String(We.x)),i.setAttribute("y2",String(We.y-22)),t.appendChild(i);let s=this._doc.createElementNS(He,"rect");s.setAttribute("class","hw-rna-builder__slot-shape"),s.setAttribute("x",String(-18)),s.setAttribute("y",String(-18)),s.setAttribute("width",String(36)),s.setAttribute("height",String(36)),s.setAttribute("rx","8"),s.setAttribute("ry","8");let n=this._buildSlot("sugar","Pick sugar (backbone)",Ve,s),r=this._doc.createElementNS(He,"circle");r.setAttribute("class","hw-rna-builder__slot-shape"),r.setAttribute("cx","0"),r.setAttribute("cy","0"),r.setAttribute("r",String(18));let o=this._buildSlot("linker","Pick linker",Ue,r),l=this._doc.createElementNS(He,"path");l.setAttribute("class","hw-rna-builder__slot-shape"),l.setAttribute("d","M -22 0 L 0 -22 L 22 0 L 0 22 Z");let a=this._buildSlot("base","Pick base",We,l);return t.appendChild(o.groupEl),t.appendChild(n.groupEl),t.appendChild(a.groupEl),this._slots.set("sugar",n),this._slots.set("linker",o),this._slots.set("base",a),t}_buildSlot(t,e,i,s){let n=this._doc.createElementNS(He,"g");n.setAttribute("class","hw-rna-builder__slot"),n.setAttribute("data-slot",t),n.setAttribute("data-testid",`rna-builder-slot-${t}`),n.setAttribute("role","button"),n.setAttribute("tabindex","0"),n.setAttribute("aria-label",e),n.setAttribute("aria-pressed","false"),n.setAttribute("transform",`translate(${i.x} ${i.y})`),n.appendChild(s);let r=this._doc.createElementNS(He,"text");r.setAttribute("class","hw-rna-builder__slot-label"),r.setAttribute("data-testid",`rna-builder-${t}-value`),r.setAttribute("x","0"),r.setAttribute("y","0"),r.setAttribute("text-anchor","middle"),r.setAttribute("dominant-baseline","central"),n.appendChild(r);let o=e=>{e.stopPropagation(),this.startPickMode(t)};return n.addEventListener("click",o),n.addEventListener("keydown",t=>{let e=t;("Enter"===e.key||" "===e.key)&&o(t)}),n.addEventListener("mouseenter",e=>this._showSlotTooltip(t,e)),n.addEventListener("mouseleave",()=>this._hideSlotTooltip()),n.addEventListener("focus",()=>this._showSlotTooltip(t,null)),n.addEventListener("blur",()=>this._hideSlotTooltip()),{id:t,biotype:Be[t],groupEl:n,shapeEl:s,labelEl:r,value:""}}_setLabelText(t,e){let i=[];for(let e=t.firstChild;null!==e;e=e.nextSibling)"title"===e.nodeName||"TITLE"===e.nodeName||i.push(e);for(let e of i)t.removeChild(e);let s=function(t){let e=t.length;return e<=2?16:e<=4?11:e<=7?8:e<=10?6:5}(e);t.setAttribute("font-size",String(s)),t.setAttribute("text-anchor","middle"),t.setAttribute("dominant-baseline","central");let n=e.length>10?`${e.slice(0,9)}…`:e;t.appendChild(this._doc.createTextNode(n));let r=t.parentNode;if(null!==r){let t=null;for(let e=r.firstChild;null!==e;e=e.nextSibling)if("title"===e.nodeName||"TITLE"===e.nodeName){t=e;break}for(null===t&&(t=this._doc.createElementNS(He,"title"),r.insertBefore(t,r.firstChild));null!==t.firstChild;)t.removeChild(t.firstChild);t.appendChild(this._doc.createTextNode(e))}}_repaintSlotColors(){for(let t of this._slots.values())this._repaintSlot(t)}_repaintSlot(t){let e=this._editor.getService().monomerLib,i=this._theme(),s=""===t.value?null:function(t,e,i){return t.getMonomerSet(e).get(i)??null}(e,t.biotype,t.value),n=ie(s,t.biotype,i.colorTheme);t.shapeEl.style.fill=n.background,t.shapeEl.style.stroke=n.line,t.labelEl.style.fill=n.text}_populateDefaults(){let t=this._editor.getService().monomerLib;for(let[e,i]of this._slots.entries()){let s=qe(t,i.biotype),n=Ke(s,Ge[e]),r=""!==i.value&&s.some(t=>t.symbol===i.value)?i.value:n??s[0]?.symbol??"";i.value=r,this._setLabelText(i.labelEl,r)}}_updatePreview(){let t=this.getSelection();for(;null!==this._preview.firstChild;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(""===t.preview?"-":t.preview)),this._updateFavStar(t)}_updateFavStar(t){if(null===this._favStar||null===this._favHooks)return;let e=""!==t.preview,i=e&&this._favHooks.isFavoriteTriplet(t.sugar,t.base,t.linker);for(;null!==this._favStar.firstChild;)this._favStar.removeChild(this._favStar.firstChild);this._favStar.appendChild(this._doc.createTextNode(i?"★":"☆")),this._favStar.setAttribute("aria-pressed",i?"true":"false"),e?this._favStar.removeAttribute("aria-disabled"):this._favStar.setAttribute("aria-disabled","true");let s="hw-rna-builder__fav"+(i?" hw-rna-builder__fav--active":"")+(e?"":" hw-rna-builder__fav--disabled");this._favStar.setAttribute("class",s)}_onAddClicked(){let t=this.getSelection();""!==t.preview&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)}_exitPickMode(){if(null===this._pickMode)return;let t=this._pickMode;this._setSlotPressed(t,!1),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null})}_setHintActive(t){let e=this._hintEl;for(;null!==e.firstChild;)e.removeChild(e.firstChild);if(null===t)return void e.setAttribute("hidden","");e.removeAttribute("hidden");let i="sugar"===t?"sugar":"base"===t?"base":"linker";e.appendChild(this._doc.createTextNode(`Pick ${i} from palette`))}_setSlotPressed(t,e){let i=this._slots.get(t);if(void 0===i)return;i.groupEl.setAttribute("aria-pressed",e?"true":"false");let s=(i.groupEl.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-rna-builder__slot--active"!==t).join(" ");i.groupEl.setAttribute("class",e?`${s} hw-rna-builder__slot--active`:s)}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_builderRdkitSvgFor(e){if(null===e)return null;let i=e.smiles;if(void 0===i||""===i)return null;let s=this._rdkit();if(null===s)return null;let n=`${e.polymerType}:${e.symbol}`;if(this._builderRdkitCache.has(n))return this._builderRdkitCache.get(n)??null;let r=ke(s,i,220,140);if(this._builderRdkitCache.size>=t._BUILDER_RDKIT_CACHE_LIMIT){let t=this._builderRdkitCache.keys().next().value;void 0!==t&&this._builderRdkitCache.delete(t)}return this._builderRdkitCache.set(n,r),r}_slotHint(t){switch(t){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(t,e){let i=""===e?"?":e;switch(t){case"sugar":return`Sugar: ${i}`;case"base":return`Base: ${i}`;case"linker":return`Linker: ${i}`}}_showSlotTooltip(t,e){let i=this._slots.get(t);if(void 0===i)return;let s=this._editor.getService().monomerLib.getMonomerSet(i.biotype),n=""===i.value?null:s.get(i.value)??null,r=Se(this._doc,"builder-tooltip","hw-builder-tooltip");$e(this._doc,r,{symbol:this._slotTitle(t,i.value),name:n?.name??"",rdkitSvg:this._builderRdkitSvgFor(n),rdkitTestid:"builder-tooltip-rdkit-svg",hint:this._slotHint(t)});let o=e;if(null!==o&&"number"==typeof o.clientX&&"number"==typeof o.clientY)Ie(r,o.clientX,o.clientY);else{let t=i.groupEl,e="function"==typeof t.getBoundingClientRect?t.getBoundingClientRect():null;null!==e?Ie(r,e.left+e.width/2,e.top+e.height/2):Ie(r,0,0)}}_hideSlotTooltip(){Me(this._doc.body.querySelector('[data-testid="builder-tooltip"]'))}};Ye._BUILDER_RDKIT_CACHE_LIMIT=256;var ze=Ye;function qe(t,e){let i=t.getMonomerSet(e),s=[];for(let t of i.values())s.push(t);return s.sort((t,e)=>t.symbol.localeCompare(e.symbol)),s}function Ke(t,e){let i=new Set;for(let e of t)i.add(e.symbol);for(let t of e)if(i.has(t))return t;return null}var je="Favorites",Qe={[je]:"★ Favorites",[It.PEPTIDE]:"Peptides",[It.RNA]:"RNA",[It.CHEM]:"CHEM",[It.BLOB]:"BLOB",G:"G"},Xe=[je,It.PEPTIDE,It.RNA,It.CHEM,It.BLOB,"G"],Je="hwe:palette:favorites",Ze="hwe:palette:active-tab";function ti(t){return`${t.sugar}|${t.base}|${t.linker}`}var ei=class t{constructor(t,e,i){this.favoritesChanged=new Mt,this._nextAddUnsub=()=>{},this._favorites=new Set,this._favoriteTriplets=[],this._pendingRnaSelection=null,this._visibleTabs=[je],this._activeTab=je,this._searchInput=null,this._filter="",this._destroyed=!1,this._rnaBuilder=null,this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,this._pickEscapeListener=null,this._pickOutsideClickListener=null,this._paletteRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??Ee(t),this._opts={documentImpl:this._doc,groupByNaturalAnalog:i?.groupByNaturalAnalog??!0,allowFavorites:i?.allowFavorites??!0},this._loadFavorites(),this._activeTab=this._resolveInitialTab(i?.initialTab),this.element=Pe(this._doc,"div",{class:"hw-palette","data-testid":"palette"}),t.appendChild(this.element),this._render(),this._libUnsub=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),this._themeUnsub=e.on("theme:change",()=>{this._destroyed||this.refresh()}),this._nextAddUnsub=e.on("option:change",t=>{this._destroyed||"nextAdd"===t.key&&this._updatePrimedClasses()})}refresh(){this._render()}setFilter(t){this._filter=t.trim().toLowerCase(),null!==this._searchInput&&this._searchInput.value!==t&&(this._searchInput.value=t),this._applyFilter()}setActiveTab(t){this._visibleTabs.includes(t)&&(this._activeTab=t,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter())}getActiveTab(){return this._activeTab}getFavorites(){let t=this._editor.getService().monomerLib,e=[];for(let i of this._favorites)null!==this._findMonomer(t,i)&&e.push(i);return e}setFavorite(t,e){e!==this._favorites.has(t)&&(e?this._favorites.add(t):this._favorites.delete(t),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}clearFavorites(){0===this._favorites.size&&0===this._favoriteTriplets.length||(this._favorites.clear(),this._favoriteTriplets.length=0,this._saveFavorites(),this._render(),this._emitFavoritesChanged())}getFavoriteTriplets(){return this._favoriteTriplets.map(t=>({...t}))}isFavoriteTriplet(t,e,i){let s=ti({sugar:t,base:e,linker:i});return this._favoriteTriplets.some(t=>ti(t)===s)}setFavoriteTriplet(t,e,i,s){let n=ti({sugar:t,base:e,linker:i}),r=this._favoriteTriplets.findIndex(t=>ti(t)===n);s!==r>=0&&(s?this._favoriteTriplets.push({sugar:t,base:e,linker:i}):this._favoriteTriplets.splice(r,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}_hidePaletteTooltips(){let t=this._doc.body;Me(t.querySelector('[data-testid="palette-tooltip"]')),Me(t.querySelector('[data-testid="palette-triplet-tooltip"]'))}_emitFavoritesChanged(){this.favoritesChanged.next({favorites:this.getFavorites(),triplets:this.getFavoriteTriplets()})}destroy(){this._destroyed||(this._destroyed=!0,null!==this._rnaBuilder&&(this._rnaBuilder.destroy(),this._rnaBuilder=null),this._libUnsub(),this._themeUnsub(),this._nextAddUnsub(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}getRnaBuilder(){return this._rnaBuilder}hasActiveBiotypeFilter(){return null!==this._activeBiotypeFilter}getActiveBiotypeFilter(){return this._activeBiotypeFilter}cancelBiotypeFilter(){if(null===this._activeBiotypeFilter)return;let t=this._pickCanceller;this._teardownPickMode(),t?.()}_buildPaletteFilterHooks(){return{beginBiotypeFilter:(t,e,i)=>{null!==this._activeBiotypeFilter&&this._teardownPickMode(),this._activeBiotypeFilter=t,this._pickResolver=e,this._pickCanceller=i,this._applyFilter();let s=t=>{"Escape"===t.key&&this.cancelBiotypeFilter()};this._pickEscapeListener=s,this._doc.defaultView?.addEventListener("keydown",s);let n=t=>{if(null===this._activeBiotypeFilter)return;let e=t.target;if(null==e)return;let i=this._activeBiotypeFilter,s=e;for(;null!==s;){let t=void 0===s.getAttribute?null:s.getAttribute("class");if(null!==t){let e=t.split(/\s+/);if(e.includes("hw-palette__tile")){if((s.getAttribute("data-biotype")??"")===i)return;break}if(e.includes("hw-rna-builder__slot")){if(this._isInsideOwnPalette(s))return;break}}s=s.parentElement}this.cancelBiotypeFilter()};this._pickOutsideClickListener=n,this._doc.addEventListener("mousedown",n,!0)},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let t=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`);if(null===t)return;let e=t;try{if("function"==typeof e.scrollTo)return void e.scrollTo({top:0,behavior:"smooth"})}catch{}"number"==typeof e.scrollTop&&(e.scrollTop=0)}_isInsideOwnPalette(t){let e=t;for(;null!==e;){if(e===this.element)return!0;e=e.parentElement}return!1}_teardownPickMode(){null!==this._activeBiotypeFilter&&(this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,null!==this._pickEscapeListener&&(this._doc.defaultView?.removeEventListener("keydown",this._pickEscapeListener),this._pickEscapeListener=null),null!==this._pickOutsideClickListener&&(this._doc.removeEventListener("mousedown",this._pickOutsideClickListener,!0),this._pickOutsideClickListener=null),this._applyFilter())}_render(){for(null!==this._rnaBuilder&&(this._pendingRnaSelection=this._rnaBuilder.getSelection(),this._rnaBuilder.destroy(),this._rnaBuilder=null);null!==this.element.firstChild;)this.element.removeChild(this.element.firstChild);let t=this._doc.createElement("input");t.setAttribute("type","search"),t.setAttribute("class","hw-palette__search"),t.setAttribute("placeholder","Search monomers..."),t.setAttribute("data-testid","palette-search"),""!==this._filter&&(t.value=this._filter),t.addEventListener("input",()=>this.setFilter(t.value)),this._searchInput=t,this.element.appendChild(t),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=je);let e=Pe(this._doc,"div",{class:"hw-palette__tabs",role:"tablist","data-testid":"palette-tabs"});for(let t of this._visibleTabs){let i=t===this._activeTab,s=Pe(this._doc,"button",{class:"hw-palette__tab",type:"button",role:"tab","aria-controls":`hw-palette-pane-${t}`,"aria-selected":i?"true":"false","data-testid":`palette-tab-${t}`,"data-tab":t,title:Qe[t]},[Qe[t]]);s.addEventListener("click",()=>this.setActiveTab(t)),e.appendChild(s)}this.element.appendChild(e);let i=Pe(this._doc,"div",{class:"hw-palette__panes"}),s=this._theme(),n=this._editor.getService().monomerLib;for(let t of this._visibleTabs){let e=t===this._activeTab,r=Pe(this._doc,"div",{class:"hw-palette__pane",id:`hw-palette-pane-${t}`,role:"tabpanel","data-testid":`palette-pane-${t}`,"data-tab":t,hidden:!e});t===je?this._buildFavoritesPane(r,n,s):this._buildPolymerPane(r,t,n,s),i.appendChild(r)}this.element.appendChild(i),this._applyFilter()}_computeVisibleTabs(){let t=this._editor.getService().monomerLib,e=new Set;for(let i of t.getPolymerTypes())e.add(i);let i=[];i.push(je);for(let t of Xe)t!==je&&e.has(t)&&i.push(t);return i}_buildFavoritesPane(t,e,i){let s=this._resolveFavoriteMonomers(e),n=this._favoriteTriplets;if(0===s.length&&0===n.length){let e=Pe(this._doc,"div",{class:"hw-palette__placeholder","data-testid":"palette-favorites-empty"},["No favorites yet — click the ☆ on any tile to add one."]);return void t.appendChild(e)}for(let[e,i]of this._groupByPolymerAndType(s))t.appendChild(this._renderGroup(e,i));n.length>0&&t.appendChild(this._renderTripletGroup("RNA · Triplets",n,e))}_groupByPolymerAndType(t){let e=new Map;for(let i of t){let t=i.polymerType,s=i.monomerType??"Undefined",n=`${t}|${s}`,r=e.get(n);void 0===r&&(r={pt:t,mt:s,list:[]},e.set(n,r)),r.list.push(i)}let i=t=>{let e=Xe.indexOf(t);return e<0?99:e},s={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(e.values()).sort((t,e)=>i(t.pt)-i(e.pt)||(s[t.mt]??9)-(s[e.mt]??9)||t.mt.localeCompare(e.mt)).map(t=>[`${this._polymerLabel(t.pt)} · ${t.mt}`,t.list])}_polymerLabel(t){return Qe[t]??t}_renderTripletGroup(t,e,i){let s=Pe(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),n=Pe(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),r=Pe(this._doc,"div",{class:"hw-triplet-chips","data-testid":"palette-triplet-favorites"});for(let t of e)r.appendChild(this._renderTripletChip(t,i));return s.appendChild(n),s.appendChild(r),s}_renderTripletChip(t,e){let i=De(t.sugar,t.base,t.linker),s=e.getMonomerSet(Et).get(t.base)??null,n=ie(s,Et,this._theme().colorTheme),r=this.isFavoriteTriplet(t.sugar,t.base,t.linker),o=void 0!==s?.name&&""!==s.name?`${i} — ${s.name}`:i,{root:l}=function(t,e){let i=!1!==e.showStar,s=Pe(t,"span",{class:"hw-triplet-chip__star"},[e.favorite?"★":"☆"]),n=Pe(t,"span",{class:"hw-triplet-chip__label"},[e.label]),r=["hw-triplet-chip"];e.favorite&&r.push("hw-triplet-chip--favorite");let o=i?[s,n]:[n];return{root:Pe(t,"div",{class:r.join(" "),role:"button",tabindex:"0","aria-label":e.title,"data-sugar":e.sugar,"data-base":e.base,"data-linker":e.linker,"data-triplet":e.label,"data-testid":`palette-triplet-${e.label}`,title:e.title,style:`background:${e.background};color:${e.textColor};`},o),star:s}}(this._doc,{sugar:t.sugar,base:t.base,linker:t.linker,label:i,title:o,background:Gt(n.background),textColor:n.text,favorite:r,showStar:this._opts.allowFavorites});return this._wireTripletChip(l,t),l}_wireTripletChip(t,e){t.addEventListener("mouseenter",t=>{let i=t,s=Se(this._doc,"palette-triplet-tooltip","hw-palette-tooltip hw-triplet-tooltip");(function(t,e,i){for(;null!==e.firstChild;)e.removeChild(e.firstChild);e.appendChild(Pe(t,"div",{class:"hw-tooltip__symbol"},[i.title]));let s=Pe(t,"div",{class:"hw-tooltip__triplet"});for(let e of i.parts){let n=Pe(t,"div",{class:"hw-tooltip__triplet-part"});if(n.appendChild(Pe(t,"div",{class:"hw-tooltip__triplet-role"},[`${e.role}: ${e.symbol}`])),void 0!==e.name&&""!==e.name&&e.name!==e.symbol&&n.appendChild(Pe(t,"div",{class:"hw-tooltip__name"},[e.name])),void 0!==e.rdkitSvg&&null!==e.rdkitSvg&&""!==e.rdkitSvg){let s={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(s["data-testid"]=i.rdkitTestid);let r=Pe(t,"div",s);r.innerHTML=e.rdkitSvg,n.appendChild(r)}s.appendChild(n)}e.appendChild(s),void 0!==i.hint&&""!==i.hint&&e.appendChild(Pe(t,"div",{class:"hw-tooltip__hint"},[i.hint]))})(this._doc,s,{title:De(e.sugar,e.base,e.linker),parts:this._tripletTooltipParts(e),hint:"Click to add this triplet",rdkitTestid:"palette-triplet-tooltip-rdkit-svg"}),Ie(s,"number"==typeof i.clientX?i.clientX:0,"number"==typeof i.clientY?i.clientY:0)}),t.addEventListener("mouseleave",()=>{Me(this._doc.body.querySelector('[data-testid="palette-triplet-tooltip"]'))}),t.addEventListener("click",t=>{let i=t.target;if(this._opts.allowFavorites&&!0===i?.classList?.contains("hw-triplet-chip__star"))return this.setFavoriteTriplet(e.sugar,e.base,e.linker,!this.isFavoriteTriplet(e.sugar,e.base,e.linker)),void t.stopPropagation();this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)}),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)})}_buildRnaDefaultChips(e){let i=this._pickSymbol(e.getMonomerSet(At),["r","R"]),s=this._pickSymbol(e.getMonomerSet(Pt),["p","P"]),n=e.getMonomerSet(Et);if(null===i||null===s)return null;let r=t._DEFAULT_TRIPLET_BASES.filter(t=>n.has(t));if(0===r.length)return null;let o=Pe(this._doc,"div",{class:"hw-triplet-chips hw-triplet-chips--defaults","data-testid":"rna-default-triplets"});for(let t of r)o.appendChild(this._renderTripletChip({sugar:i,base:t,linker:s},e));return o}_tripletTooltipParts(t){let e=this._editor.getService().monomerLib,i=(t,i,s)=>{let n=e.getMonomerSet(i).get(s)??null;return{role:t,symbol:s,...void 0!==n?.name?{name:n.name}:{},rdkitSvg:null===n?null:this._paletteRdkitSvg(n)}};return[i("Sugar",At,t.sugar),i("Base",Et,t.base),i("Linker",Pt,t.linker)]}_pickSymbol(t,e){for(let i of e)if(t.has(i))return i;let i=t.keys().next();return!0===i.done?null:i.value}_restoreRnaSelection(){let t=this._pendingRnaSelection;if(this._pendingRnaSelection=null,null===t||null===this._rnaBuilder)return;let e=this._editor.getService().monomerLib;""!==t.sugar&&e.getMonomerSet(At).has(t.sugar)&&this._rnaBuilder.setField("sugar",t.sugar),""!==t.base&&e.getMonomerSet(Et).has(t.base)&&this._rnaBuilder.setField("base",t.base),""!==t.linker&&e.getMonomerSet(Pt).has(t.linker)&&this._rnaBuilder.setField("linker",t.linker)}_resolveFavoriteMonomers(t){let e=[];for(let i of this._favorites){let s=this._findMonomer(t,i);null!==s&&e.push(s)}return e}_findMonomer(t,e){for(let i of t.getPolymerTypes()){let s=t.getMonomer(i,e);if(null!==s)return s}return null}_buildPolymerPane(t,e,i,s){let n=e,r=this._monomersForPolymer(n,i);if(0===r.length)return;if(n===It.RNA){this._rnaBuilder=new ze(t,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(t,e,i)=>this.isFavoriteTriplet(t,e,i),toggleFavoriteTriplet:(t,e,i)=>this.setFavoriteTriplet(t,e,i,!this.isFavoriteTriplet(t,e,i))}:null}),this._restoreRnaSelection();let e=this._buildRnaDefaultChips(i);null!==e&&t.appendChild(e);let s=this._groupRna(r);for(let[e,i]of s)0!==i.length&&t.appendChild(this._renderGroup(e,i));return}if(n===It.PEPTIDE&&this._opts.groupByNaturalAnalog){let e=this._groupByAnalog(r);for(let[i,s]of e){let e=""===i?"Other":i;t.appendChild(this._renderGroup(e,s))}return}let o=Pe(this._doc,"div",{class:"hw-palette__group-tiles"}),l=this._editor.getNextAddSymbol(),a=this._sortByColor(r);for(let t of a){let e=this._biotype(t,n);o.appendChild(this._renderTile(t,e,l))}t.appendChild(o)}_renderGroup(t,e){let i=Pe(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),s=Pe(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),n=Pe(this._doc,"div",{class:"hw-palette__group-tiles"}),r=this._editor.getNextAddSymbol(),o=this._sortByColor(e);for(let t of o){let e=this._biotype(t,t.polymerType);n.appendChild(this._renderTile(t,e,r))}return i.appendChild(s),i.appendChild(n),i}_sortByColor(t){let e=this._theme(),i=t.map((t,i)=>{let s=function(t){let e=Ot(t);if(null===e)return{h:0,s:0,l:0};let[i,s,n]=Dt(e[0],e[1],e[2]);return{h:i,s,l:n}}(ie(t,this._biotype(t,t.polymerType),e.colorTheme).background),n=0===s.s?1:0;return{m:t,idx:i,h:s.h,s:s.s,l:s.l,isGrey:n}});return i.sort((t,e)=>t.isGrey!==e.isGrey?t.isGrey-e.isGrey:t.h!==e.h?t.h-e.h:t.s!==e.s?t.s-e.s:t.l!==e.l?t.l-e.l:t.idx-e.idx),i.map(t=>t.m)}_monomersForPolymer(t,e){let i=e.getMonomerSymbolsByType(t),s=[];for(let n of i){let i=e.getMonomer(t,n);null!==i&&s.push(i)}return s.sort((t,e)=>t.symbol.localeCompare(e.symbol)),s}_groupByAnalog(t){let e=new Map;for(let i of t){let t=i.naturalAnalog??"",s=e.get(t);void 0===s&&(s=[],e.set(t,s)),s.push(i)}let i=[],s=Array.from(e.keys()).sort((t,e)=>""===t&&""!==e?1:""===e&&""!==t?-1:t.localeCompare(e));for(let t of s)i.push([t,e.get(t)]);return new Map(i)}_groupRna(t){let e=[],i=[],s=[],n=[];for(let r of t){let t=se(r);t===At?e.push(r):t===Et?i.push(r):t===Pt?s.push(r):n.push(r)}let r=new Map;return r.set("Backbones",e),r.set("Bases",i),r.set("Linkers",s),n.length>0&&r.set("Other",n),r}_renderTile(t,e,i){let s=this._favorites.has(t.symbol),n=null!==i&&i.symbol===t.symbol&&i.biotype===e,{root:r,star:o}=function(t,e){let i=ie(e.monomer,e.biotype,e.theme.colorTheme),s=Gt(i.background),n=i.text,r=function(t,e){let i=Vt(t),s=Vt(e);return(Math.max(i,s)+.05)/(Math.min(i,s)+.05)}(n,s)<5,o=e.monomer.symbol,l=function(t){return t<=3?14:t<=6?11:t<=9?9:8}(o.length),a=`font-size:${l}px;${o.length>=10?"line-height:1.1;letter-spacing:-0.02em;":""}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:80px;display:inline-block;`,c=Pe(t,"span",{class:"hw-palette__star"},[e.favorite?"★":"☆"]),h=Pe(t,"span",{class:"hw-palette__label",style:a},[o]),d=["hw-palette__tile"];e.primed&&d.push("hw-palette__tile--primed"),e.favorite&&d.push("hw-palette__tile--favorite"),r&&d.push("hw-palette__tile--low-contrast");let u=void 0!==e.monomer.name?`${o} — ${e.monomer.name}`:o,p=`background:${s};color:${n};width:100%;min-width:48px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return{root:Pe(t,"div",{class:d.join(" "),draggable:"true",role:"button","aria-pressed":e.primed?"true":"false","aria-label":u,"data-symbol":o,"data-biotype":e.biotype,"data-bg":s,"data-raw-bg":i.background,"data-testid":`palette-tile-${o}`,title:u,style:p},[c,h]),star:c}}(this._doc,{monomer:t,biotype:e,theme:this._theme(),favorite:s,primed:n});return this._wireTile(r,o,t,e),r}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_paletteRdkitSvg(e){let i=e.smiles;if(void 0===i||""===i)return null;let s=this._rdkit();if(null===s)return null;let n=`${e.polymerType}:${e.symbol}`;if(this._paletteRdkitCache.has(n))return this._paletteRdkitCache.get(n)??null;let r=ke(s,i,220,140);if(this._paletteRdkitCache.size>=t._PALETTE_RDKIT_CACHE_LIMIT){let t=this._paletteRdkitCache.keys().next().value;void 0!==t&&this._paletteRdkitCache.delete(t)}return this._paletteRdkitCache.set(n,r),r}_wireTile(t,e,i,s){t.addEventListener("mouseenter",t=>{let e=t,s=Se(this._doc,"palette-tooltip","hw-palette-tooltip");$e(this._doc,s,{symbol:i.symbol,name:i.name??"",rdkitSvg:this._paletteRdkitSvg(i),rdkitTestid:"palette-tooltip-rdkit-svg"}),Ie(s,"number"==typeof e.clientX?e.clientX:0,"number"==typeof e.clientY?e.clientY:0)}),t.addEventListener("mouseleave",()=>{Me(this._doc.body.querySelector('[data-testid="palette-tooltip"]'))}),t.addEventListener("click",t=>{let e=t.target;if(this._opts.allowFavorites&&void 0!==e&&!0===e?.classList?.contains("hw-palette__star"))return this.setFavorite(i.symbol,!this._favorites.has(i.symbol)),void t.stopPropagation();if(null!==this._activeBiotypeFilter&&this._activeBiotypeFilter===s){let e=this._pickResolver;return this._teardownPickMode(),e?.(i.symbol),this._scrollActivePaneToTop(),void t.stopPropagation()}let n=this._editor.getSelection();if(n.atoms.size>0){let e=this._editor.getMol(),r=[];for(let t of n.atoms){let i=e.atoms.find(e=>e.id===t);void 0!==i&&r.push(i)}return r.length>0&&r.every(t=>t.biotype===s)?(this._editor.replaceMonomers(r,i.symbol),void t.stopPropagation()):(this._editor.fire("editor:status",{message:`Cannot bulk-replace ${r.length} selected atom(s) with ${i.symbol}: selection contains incompatible biotypes for ${s}.`,severity:"warn",durationMs:3e3}),void t.stopPropagation())}let r=this._editor.getNextAddSymbol();if(null!==r&&r.symbol===i.symbol&&r.biotype===s)return this._editor.setNextAddSymbol(null),void this._updatePrimedClasses();this._editor.setNextAddSymbol(i.symbol,s),this._updatePrimedClasses()}),t.addEventListener("dragstart",t=>{let e=t.dataTransfer;if(null!=e)try{e.setData("application/x-hwe-monomer",JSON.stringify({symbol:i.symbol,biotype:s})),e.effectAllowed="copy"}catch{}Me(this._doc.body.querySelector('[data-testid="palette-tooltip"]')),this._editor.startPaletteDrag(i.symbol,s)})}_biotype(t,e){let i=se(t);if(null!==i)return i;switch(e){case It.PEPTIDE:return xt;case It.RNA:return At;case It.CHEM:return kt;case It.BLOB:return St;default:return kt}}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_applyFilter(){let t=this._filter,e=this._activeBiotypeFilter,i=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`),s=(i??this.element).querySelectorAll(".hw-palette__tile");for(let i=0;i<s.length;i++){let n=s[i],r=(n.getAttribute("data-symbol")??"").toLowerCase(),o=(n.getAttribute("title")??"").toLowerCase(),l=n.getAttribute("data-biotype")??"",a=(""===t||r.indexOf(t)>=0||o.indexOf(t)>=0)&&(null===e||l===e);n.style.display=a?"":"none"}let n=(i??this.element).querySelectorAll(".hw-triplet-chip");for(let i=0;i<n.length;i++){let s=n[i],r=[s.getAttribute("data-triplet")??"",s.getAttribute("data-sugar")??"",s.getAttribute("data-base")??"",s.getAttribute("data-linker")??""].join(" ").toLowerCase(),o=(""===t||r.indexOf(t)>=0)&&null===e;s.style.display=o?"":"none"}let r=(i??this.element).querySelectorAll(".hw-palette__group");for(let t=0;t<r.length;t++){let e=r[t],i=e.querySelectorAll(".hw-palette__tile, .hw-triplet-chip"),s=!1;for(let t=0;t<i.length;t++)if("none"!==i[t].style.display){s=!0;break}s?(e.removeAttribute("hidden"),e.removeAttribute("data-section-empty")):(e.setAttribute("hidden",""),e.setAttribute("data-section-empty","true"))}}_updatePrimedClasses(){let t=this._editor.getNextAddSymbol(),e=this.element.querySelectorAll(".hw-palette__tile");for(let i=0;i<e.length;i++){let s=e[i],n=s.getAttribute("data-symbol")??"",r=s.getAttribute("data-biotype")??"",o=null!==t&&t.symbol===n&&t.biotype===r,l=(s.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-palette__tile--primed"!==t).join(" ");s.setAttribute("class",o?`${l} hw-palette__tile--primed`:l),s.setAttribute("aria-pressed",o?"true":"false")}}_applyActiveTabClasses(){let t=this.element.querySelectorAll(".hw-palette__tab");for(let e=0;e<t.length;e++){let i=t[e],s=i.getAttribute("data-tab")??"";i.setAttribute("aria-selected",s===this._activeTab?"true":"false")}let e=this.element.querySelectorAll(".hw-palette__pane");for(let t=0;t<e.length;t++){let i=e[t];(i.getAttribute("data-tab")??"")===this._activeTab?i.removeAttribute("hidden"):i.setAttribute("hidden","")}}_localStorage(){if(!this._opts.allowFavorites)return null;let t=this._doc.defaultView;if(null==t)return null;try{return t.localStorage??null}catch{return null}}_resolveInitialTab(t){if(void 0!==t&&Xe.includes(t))return t;let e=this._localStorage();if(null!==e)try{let t=e.getItem(Ze);if(null!==t&&Xe.includes(t))return t}catch{}return je}_persistActiveTab(){let t=this._localStorage();if(null!==t)try{t.setItem(Ze,this._activeTab)}catch{}}_loadFavorites(){let t=this._localStorage();if(null!==t){try{let e=t.getItem(Je);if(null!==e&&""!==e){let t=JSON.parse(e),i=this._extractSymbols(t);for(let t of i)this._favorites.add(t);for(let e of this._extractTriplets(t))this._favoriteTriplets.push(e);return}}catch{}try{let e=t.getItem("hwe.palette.favorites");if(null===e||""===e)return;let i=JSON.parse(e);if(Array.isArray(i)){for(let t of i){if("string"!=typeof t)continue;let e=t.indexOf("|"),i=e>=0?t.slice(e+1):t;""!==i&&this._favorites.add(i)}this._saveFavorites()}}catch{}}}_extractSymbols(t){if(Array.isArray(t)){let e=[];for(let i of t)"string"==typeof i&&e.push(i);return e}if(null!==t&&"object"==typeof t){let e=t;if(Array.isArray(e.symbols)){let t=[];for(let i of e.symbols)"string"==typeof i&&t.push(i);return t}}return[]}_extractTriplets(t){if(null===t||"object"!=typeof t)return[];let e=t;if(!Array.isArray(e.triplets))return[];let i=[];for(let t of e.triplets){if(null===t||"object"!=typeof t)continue;let e=t;"string"==typeof e.sugar&&"string"==typeof e.base&&"string"==typeof e.linker&&i.push({sugar:e.sugar,base:e.base,linker:e.linker})}return i}_saveFavorites(){let t=this._localStorage();if(null!==t)try{let e={symbols:Array.from(this._favorites)};this._favoriteTriplets.length>0&&(e.triplets=this._favoriteTriplets.map(t=>({...t}))),t.setItem(Je,JSON.stringify(e))}catch{}}};ei._DEFAULT_TRIPLET_BASES=["A","C","G","U","T"],ei._PALETTE_RDKIT_CACHE_LIMIT=256;new Set([It.PEPTIDE,It.RNA,It.CHEM,It.BLOB]),new Set(["Backbone","Branch","Terminal","Undefined"]);var ii,si,ni;function ri(e,i=!0){if(null==e)return"rgb(100,100,100)";const s=t.Color.fromHtml(e);if(i){const e=t.Color.g(s),i=t.Color.r(s),n=t.Color.b(s),r=Math.sqrt(Math.pow(0-i,2)+Math.pow(0-e,2)+Math.pow(0-n,2));if(r>210)return`rgb(${i/r*210},${e/r*210},${n/r*210})`}return t.Color.toRgb(s)}!function(t){t[t.default=0]="default",t[t.continuous=1]="continuous"}(ii||(ii={})),function(t){t.Sequence="sequence",t.Helm="notation",t.Properties="properties",t.StructureView="structureview"}(si||(si={}));class oi{static hashCode(t){let e=0;if(0===t.length)return e;for(let i=0;i<t.length;i++)e=(e<<5)-e+t.charCodeAt(i),e|=0;return e}}class li{}class ai extends li{static get palette(){return ai._pallete||(ai._pallete=ai.buildPalette()),ai._pallete}static buildPalette(){return Z().then(t=>{t.awaitLoaded(1/0).then(()=>{const e=t.getMonomerLib();e.onChanged.subscribe(()=>{ai.customMonomerColors={},ai.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const i=e.getMonomerSymbolsByType(t);for(const s of i){const i=e.getMonomer(t,s);i?.meta?.colors?.default?.background&&(this.customMonomerColors[s]||(this.customMonomerColors[s]={}),this.customMonomerColors[s][t]=ri(i.meta.colors.default.background))}}})})}),[].concat(...Object.values(yt.colourPalette))}get(t,e){const i=ai.palette.length,s=ai.customMonomerColors[t],n=e??It.PEPTIDE;if(s&&s[n])return s[n];const r=oi.hashCode(t)%i;return ri(ai.palette[r])}}ai._pallete=null,ai.customMonomerColors={},ai.polymerTypes=[],P("renderers",()=>{let e,i;k(async()=>{await Q(),e=await Z(),i=await lt(),await e.loadMonomerLibForTests()}),S(async()=>{await at(i),await e.loadMonomerLib(!0)}),w("missedInLib",async()=>{await async function(){const e=await tt.dapi.files.readCsv("System:AppData/Helm/tests/sample_HELM-missedInLib.csv"),i=e.getCol("HELM"),s=tt.shell.addTableView(e);await F(()=>ht()(s.root).find(".d4-grid canvas").length>0,"Table view canvas not found",100),await tt.data.detectSemanticTypes(e),T(i.semType,t.SEMTYPE.MACROMOLECULE),T(i.meta.units,ut.HELM),T(i.getTag(t.TAGS.CELL_RENDERER),"helm");const n=i.getTag(".cell-renderer.render.error");if(n){const t=JSON.parse(n),e=new Error(t.message);throw e.stack=t.stack,e}}()}),w("scatterPlotTooltip",async()=>{await async function(){const e=t.DataFrame.fromCsv(s);e.currentRowIdx=0;const i=tt.shell.addTableView(e);await tt.data.detectSemanticTypes(e);const n=e.plot.scatter({x:"x",y:"y"});i.dockManager.dock(n,t.DOCK_TYPE.RIGHT,null),await Promise.all([v(n.onAfterDrawScene,()=>{},()=>{n.invalidateCanvas()},1e3),X(i.grid,500)]);const r=n.root.getBoundingClientRect(),o=n.worldToScreen(1,0),l=new MouseEvent("mousemove",{cancelable:!0,bubbles:!0,view:window,button:0,clientX:r.left+o.x,clientY:r.top+o.y}),a=ht()(n.root).find("canvas").get()[0];await v((0,dt.fromEvent)(a,"mousemove"),()=>{Ti.logger.debug(`Test: event, currentRowIdx=${e.currentRowIdx}`),T(ht()(K.tooltip.root).find("div table.d4-row-tooltip-table tr td canvas").length,1),T(n.hitTest(o.x,o.y),1)},()=>{a.dispatchEvent(l)},500),await X(i.grid,1e3)}()});const s="seq,x,y\nPEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$,0,0\nRNA1{r(A)p.r(C)p.r(G)p.r(U)p}$$$$,1,0\nRNA1{d(A)p.d(C)p.d(G)p.d(U)p}|PEPTIDE1{I.H.A.N.T.Thr_PO3H2}$$$$,0,1\n"}),function(t){t.TYPE="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t[t.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",t.RGP_LINE_START="M  RGP",t.ATOM_ALIAS_LINE_START="A  ",t.END="M  END"}(ni||(ni={}));class ci{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return null!==(t=this._atomTypes)&&void 0!==t||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let i=t;const s=this.isWhitespace(i)?e:e-1;for(let t=0;t<s;t++)i=this.getNextColumnIdx(i);return i}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let i=this.getAtomBlockIdx();for(let s=0;s<t;s++)i=this.shiftIdxToAtomType(i),e[s]=this.parseAtomType(i),i=this.getNextLineIdx(i);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),i=new Float32Array(this.atomCount);let s=this.getAtomBlockIdx();for(let n=0;n<this.atomCount;n++){s=this.shiftIdxToXColumn(s);for(const r of[t,e,i])r[n]=this.parseFloatValue(s),s=this.getNextColumnIdx(s);s=this.getNextLineIdx(s)}return{x:t,y:e,z:i}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let i=0;i<this.bondCount;i++){e=this.shiftIdxToBondedAtomsPair(e);const s=new Uint16Array(2);s[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),s[1]=this.parseIntValue(e),t[i]=s,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let i=this.getBondBlockIdx();for(let s=0;s<t;s++)i=this.shiftIdxToBondType(i),e[s]=this.parseIntValue(i),i=this.getNextLineIdx(i);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let i=e+1;for(;!this.isWhitespace(i);)++i;return t(this.fileContent.substring(e,i))}}class hi extends ci{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,i=e;return this.isQuote(e)?(i=this.getNextIdenticalChar(e),e++):i=this.fileContent.indexOf(" ",i),this.fileContent.substring(e,i)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment((t,e)=>{return 39===t||34===t||76===t&&!((i=this.fileContent.charCodeAt(e+1))>64&&i<91||i>96&&i<123);var i})}isFragment(){return this.isQueryOrFragment(t=>82===t||42===t)}isQueryOrFragment(t){const e=this.atomCount;let i=this.getAtomBlockIdx();for(let s=0;s<e;s++){if(i=this.shiftIdxToAtomType(i),t(this.fileContent.charCodeAt(i),i))return!0;i=this.getNextLineIdx(i)}return!1}}class di extends hi{constructor(t){super(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map,e=this.fileContent.split("\n");e.filter(t=>t.startsWith(ni.RGP_LINE_START)).forEach(e=>{const i=this.getAtomIdxToRgpIdxList(e);for(const[e,s]of i){if(t.has(e))throw new Error(`R group ${e} is already in the map`);t.set(e,s)}});const i=e.map((t,e)=>{if(t.startsWith(ni.ATOM_ALIAS_LINE_START))return e}).filter(t=>void 0!==t),s=i.map(t=>e[t]),n=i.map(t=>e[t+1]);s.forEach((e,i)=>{const s=parseInt(e.split(/\s+/)[1])-1,r=parseInt(n[i].substring(1));if(t.has(r))throw new Error(`R group ${r} is already in the map`);t.set(r,s)});const r=this.getRGroupAtomicIndices().filter(e=>!Array.from(t.values()).includes(e));if(0!==r.length)throw new Error(`Unaccounted R group indices: ${r}`);return t}getAtomIdxToRgpIdxList(t){const e=t.split(/\s+/).filter(t=>t).slice(3).map(t=>parseInt(t)),i=new Array(e.length/2);for(let t=0;t<e.length;t+=2)i[t/2]=[e[t+1],e[t]-1];return i}getRGroupAtomicIndices(){return this.atomTypes.map((t,e)=>{if(t.includes("R#"))return e}).filter(t=>void 0!==t)}static isValidMolfile(t){return-1!==t.indexOf(ni.TYPE)&&-1!==t.indexOf(ni.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,ni.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<ni.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,ni.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,ni.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+ni.NUM_OF_COUNTS_DIGITS;const i=parseInt(this.fileContent.substring(t,e));return t=e,e+=ni.NUM_OF_COUNTS_DIGITS,{atomCount:i,bondCount:parseInt(this.fileContent.substring(t,e))}}}class pi extends hi{constructor(t){super(t),this.init(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map;return this.getAtomLines().forEach((e,i)=>{const s=e.match(/RGROUPS=\(([\d\s]+)\)/);if(s){const e=s[1].split(/\s+/).map(t=>parseInt(t));if(e.length>2)throw new Error(`R group data ${e} has more than 2 elements`);const n=e[1];if(t.has(n))throw new Error(`R group ${n} is already in the map`);t.set(n,i)}}),t}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M  V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M  V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M  V30 BEGIN BOND"))}static isValidMolfile(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M  END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M  V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const i=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:i,bondCount:parseInt(this.fileContent.substring(t,e))}}}class fi{constructor(){}static getInstance(t){if(fi.isMolfileV2K(t))return new di(t);if(fi.isMolfileV3K(t))return new pi(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return di.isValidMolfile(t)}static isMolfileV3K(t){return pi.isValidMolfile(t)}}async function gi(){const e=t.Func.find({package:"Bio",name:"getSeqHelper"});if(0===e.length)throw new Error("Package 'Bio' must be installed for SeqHelper.");return(await e[0].prepare().call()).getOutputParamValue()}P("getMolfiles",()=>{let e,i;k(async()=>{await Q(),e=await Z(),i=await lt(),await e.loadMonomerLibForTests()}),S(async()=>{await at(i),await e.loadMonomerLib(!0)}),w("linear1",async()=>{const e=t.DataFrame.fromCsv("Helm, atoms, bonds\nPEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV}$$$$,11,10\nPEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV}$$$$,11,10\nPEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$,9,8"),i=e.getCol("Helm"),s=tt.shell.addTableView(e);Ti.logger.debug("Helm/getMolfiles/linear1, grid awaiting 1"),await X(s.grid,5e3),Ti.logger.debug("Helm/getMolfiles/linear1, grid awaited 1");const n=await tt.functions.call("Helm:getMolfiles",{col:i});T(n.length,i.length);const r=n.toList().map(t=>fi.getInstance(t));E(r.map(t=>t.atomCount),e.getCol("atoms").toList()),E(r.map(t=>t.bondCount),e.getCol("bonds").toList()),Ti.logger.debug("Helm/getMolfiles/linear1, grid awaiting 2"),await X(s.grid,5e3),Ti.logger.debug("Helm/getMolfiles/linear1, grid awaited 2")})});class mi extends Error{constructor(t,e){super(t,e)}}async function yi(t,e){const i=K.div([],{style:{width:"0",height:"0"}});document.documentElement.appendChild(i);try{if(t.length>1e3)throw new mi("Too long sequence to calculate molecular properties.");const s=(e.isHelm()?t:e.getConverter(ut.HELM)(t)).replaceAll(H,"{").replaceAll(B,".").replaceAll(G,"}").replace("{*}","{}"),n=(await j()).createHelmWebEditor(i).editor;n.setHelm(s);const r=n.getFormula(!0),o=Math.round(100*n.getMolWeight())/100,l=Math.round(100*n.getExtinctionCoefficient())/100;return{formula:r.replace(/<sub>/g,"").replace(/<\/sub>/g,""),"molecular weight":o,"extinction coefficient":l}}finally{ht()(i).empty(),i.remove()}}const bi={Helm:{seq:"PEPTIDE1{I.H.A.C.T.[Thr_PO3H2].[Aca].[D-Tyr_Et]}|PEPTIDE2{E.A.[meG]}$PEPTIDE1,PEPTIDE2,4:R3-1:R1$$$V2.0",units:ut.HELM,res:{formula:"C58H94N13O21SP","molecular weight":1372.49,"extinction coefficient":1.55}},separator:{seq:"I/H/A/C/T/Thr_PO3H2/Aca/D-Tyr_Et",units:ut.SEPARATOR,separator:"/",alphabet:pt.UN,res:{formula:"C47H77N10O15SP","molecular weight":1085.22,"extinction coefficient":1.55}},separator2:{seq:"meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Aze/dV/E/N////Phe_4Me",units:ut.SEPARATOR,separator:"/",alphabet:pt.UN,res:{formula:"C91H146N19O25P","molecular weight":1937.25,"extinction coefficient":1.49}},"separator-gaps":{seq:"I/H/A//T/Thr_PO3H2/Aca/D-Tyr_Et",units:ut.SEPARATOR,separator:"/",alphabet:pt.UN,res:{formula:"C44H72N9O14P","molecular weight":982.08,"extinction coefficient":1.49}},"fasta-PT":{seq:"IHACTTAY",units:ut.FASTA,alphabet:pt.PT,res:{formula:"C38H58N10O12S","molecular weight":879,"extinction coefficient":1.55}},"fasta-RNA":{seq:"ACGUAUUCC",units:ut.FASTA,alphabet:pt.RNA,res:{formula:"C84H107N30O65P9","molecular weight":2855.69,"extinction coefficient":86.96}},"fasta-DNA":{seq:"ACGTATTCC",units:ut.FASTA,alphabet:pt.DNA,res:{formula:"C87H113N30O56P9","molecular weight":2753.78,"extinction coefficient":86.96}}};function _i(t,e,i){const s=i.parse(t);T(s.atoms.length,e.atomCount),T(s.bonds.length,e.bondCount),T(s.atoms.every(t=>!t.elem.startsWith("[")&&!t.elem.endsWith("]")),!0,"Atoms should not contain square braces.")}var Ci;P("properties-widget",()=>{let e,i,s=null;k(async()=>{await Q(),e=await gi(),i=await Z(),s=lt(),await i.loadMonomerLibForTests()}),S(async()=>{await at(s),await i.loadMonomerLib(!0)});for(const[t,e]of Object.entries(bi))w(t,async()=>{await n(e.seq,e.units,e.separator,e.alphabet,e.res)});async function n(i,s,n,r,o){const l=t.Column.fromStrings("seq",[i]);l.semType=t.SEMTYPE.MACROMOLECULE,l.meta.units=s,n&&l.setTag(ft.separator,n),r&&l.setTag(ft.alphabet,r);const a=e.getSeqHandler(l);A(await yi(i,a),o)}w("too-long",async()=>{const i=function(e=1e4){const i="meI/hHis/Aca/N//dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe".repeat(Math.ceil(e/10)).slice(0,-1),s=t.Column.fromList(t.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(i));s.semType=t.SEMTYPE.MACROMOLECULE,s.meta.units=ut.SEPARATOR,s.setTag(ft.separator,"/"),s.setTag(ft.alphabet,pt.UN),s.setTag(ft.alphabetIsMultichar,"true");const n=[];return n.push(s),n.push(t.Column.fromList(t.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),n}(),s=t.DataFrame.fromColumns(i).getCol("MSA"),n=e.getSeqHandler(s);let r=!0;try{await yi(s.get(0),n)}catch(t){t instanceof mi&&(r=!0)}T(r,!0)})}),P("parseHelm",()=>{const t={PT:{src:"PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0",tgt:{atomCount:6,bondCount:5,helm:"PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0"}},"PT-cyclic":{src:"PEPTIDE1{[meI].C.[Aca].[Cys_SEt].T.C.[Thr_PO3H2].[Aca]}$PEPTIDE1,PEPTIDE1,8:R2-1:R1$$$V2.0",tgt:{atomCount:8,bondCount:8,helm:"PEPTIDE1{[meI].C.[Aca].[Cys_SEt].T.C.[Thr_PO3H2].[Aca]}$PEPTIDE1,PEPTIDE1,8:R2-1:R1$$$V2.0"}},RNA:{src:"RNA1{[dhp]([m1A])p.r(T)p.r(T)p.r(G)p}$$$$V2.0",tgt:{atomCount:12,bondCount:11,helm:"RNA1{[dhp]([m1A])p.r(T)p.r(T)p.r(G)p}$$$$V2.0"}},"PT-with-gap":{src:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$$$$V2.0",tgt:{atomCount:8,bondCount:7,helm:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$$$$V2.0"}},"PT-with-gap-at-connection":{src:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0",tgt:{atomCount:8,bondCount:8,helm:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0"}}};let e,i,s;k(async()=>{await Q(),e=await j(),i=await Z(),s=await 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Object.entries(s))w(`${e}`,async()=>{let e=null;try{const e=t.removeGaps(i.src.helm);T(e.resHelm,i.tgt.helm),E(Array.from(e.monomerMap.entries()),i.tgt.map)}catch(t){e=t}i.tgt.errType&&T(e?.type,i.tgt.errType,"HelmNotSupportedError thrown expected")})});class vi{constructor(t,e=!0,i){return this.substructure=t,this.readOnly=e,this.logger=i,new Proxy(this,{set:(t,e,i)=>{if(this.logger?.debug(`BioFilterProps.set ${e.toString()}( '${i}' )`),this.readOnly)throw new Error("Properties are immutable.");return t[e]=i,!0}})}}P("bio-substructure-filters",async()=>{let t,e,i;async function s(t,e){if(!e.columns.names().includes(t))throw new Error(`The column '${t}' not found. 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0===s?void 0:s.every(t=>{var i;return(null===(i=t.options)||void 0===i?void 0:i.skipReason)||null!=(null==e?void 0:e.test)&&e.test.toLowerCase()!==t.name.toLowerCase()});if(!t){const t=(null!==(r=m.tests)&&void 0!==r?r:[]).filter(t=>{var i;return(null===(i=t.options)||void 0===i?void 0:i.skipReason)||null!=(null==e?void 0:e.test)&&e.test.toLowerCase()!==t.name.toLowerCase()}).length;l(`Package testing: Started {{${h}}}${t>0?` skipped {{${t}}}`:""}`),m.beforeStatus=yield y(m.before,h)}let _,C=null!==(o=m.tests)&&void 0!==o?o:[];e.stressTest&&(C=C.filter(t=>{var e;return null===(e=t.options)||void 0===e?void 0:e.stressTest}),C=O(C)),(null!==(p=null===(d=e.tags)||void 0===d?void 0:d.length)&&void 0!==p?p:0)>0&&(C=C.filter(t=>{var i,s;return null===(s=null===(i=t.options)||void 0===i?void 0:i.tags)||void 0===s?void 0:s.some(t=>{var i;return(null!==(i=null==e?void 0:e.tags)&&void 0!==i?i:[]).includes(t)})})),m.beforeStatus?(_=Array.from(C.map(t=>({date:(new 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Set),selectionLayer:xe(t,i,s)}}(t,{theme:this._currentTheme(),selectedAtomIds:e.atoms,highlightedAtomIds:this._editorHighlights()});this._spliceLayer("hw-highlights",i.highlightLayer),this._spliceLayer("hw-selections",i.selectionLayer)}_spliceLayer(t,e){let i=this._svgRoot.querySelector(`.${t}`);if(null===i||null===i.parentNode)return;let s=this._doc.createElementNS("http://www.w3.org/2000/svg","svg");s.innerHTML=e;let n=s.querySelector(`.${t}`);null!==n&&i.parentNode.replaceChild(n,i)}_editorHighlights(){let t=this._editor;return"function"==typeof t._currentHighlights?t._currentHighlights():new Set}_currentTheme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_applyResize(t,e){this._width=t,this._height=e,this._pinnedBbox=null,this._renderFresh()}_applyViewport(t){let e=this._svgRoot.querySelector(".hw-content");if(null===e)return;let i=`translate(${t.offset.x} ${t.offset.y}) scale(${t.scale})`,s=""===this._baseTransform?i:`${i} ${this._baseTransform}`;e.setAttribute("transform",s)}_showTooltip(t,e,i){let s=this._tooltip;if(null===s)return;let n=""===t.symbol?"?":t.symbol,r=t.monomer?.name??"",o=t.bio.positionInChain,l=""===t.bio.chainId?"?":t.bio.chainId,a=""!==r&&r!==n?`${r} @ ${l}:${o}`:`${n} @ ${l}:${o}`,c=this._renderRdkitTooltipSvg(t);$e(this._doc,s,{symbol:n,name:a,rdkitSvg:c,rdkitTestid:"atom-tooltip-rdkit-svg"});let h=""!==r&&r!==n?`${n} — ${r}  @ ${l}:${o}`:`${n}  @ ${l}:${o}`,d=this._doc.createElement("div");d.setAttribute("class","hw-atom-tooltip__text"),d.style.display="none",d.appendChild(this._doc.createTextNode(h)),s.appendChild(d),Ie(s,e,i)}_renderRdkitTooltipSvg(e){let i=this._editor.getService().options.rdkitModule;if(null==i)return null;let s=e.monomer;if(null===s)return null;let n=s.smiles;if(void 0===n||""===n)return null;let r=`${s.polymerType}:${s.symbol}`;if(this._rdkitSvgCache.has(r))return this._rdkitSvgCache.get(r)??null;let o=ke(i,n,220,140);if(this._rdkitSvgCache.size>=t._RDKIT_CACHE_LIMIT){let t=this._rdkitSvgCache.keys().next().value;void 0!==t&&this._rdkitSvgCache.delete(t)}return this._rdkitSvgCache.set(r,o),o}_hideTooltip(){Me(this._tooltip)}_showBondTooltip(t,e,i){let s=this._bondTooltip;if(null===s)return;let n=Oe(t.r1),r=Oe(t.r2),o=`${t.a1.symbol}@${t.a1.bio.chainId}:${t.a1.bio.positionInChain}`,l=`${t.a2.symbol}@${t.a2.bio.chainId}:${t.a2.bio.positionInChain}`;$e(this._doc,s,{symbol:`${n}-${r} (${t.kind})`,name:`${o} ↔ ${l}`}),Ie(s,e,i)}_hideBondTooltip(){Me(this._bondTooltip)}_paintBondPreview(t,e,i){let s=this._svgRoot.querySelector(".hw-content");if(null===s)return;let n=s.querySelector(".hw-bond-preview");null===n&&(n=this._doc.createElementNS("http://www.w3.org/2000/svg","line"),n.setAttribute("class","hw-bond-preview"),n.setAttribute("data-testid","bond-preview"),n.setAttribute("stroke-dasharray","6 4"),n.setAttribute("stroke-width","2"),n.setAttribute("fill","none"),n.setAttribute("pointer-events","none"),s.appendChild(n)),n.setAttribute("x1",String(t.x)),n.setAttribute("y1",String(t.y)),n.setAttribute("x2",String(e.x)),n.setAttribute("y2",String(e.y)),n.setAttribute("stroke",i?"#1f5fcd":"#999999")}_clearBondPreview(){let t=this._svgRoot.querySelector(".hw-bond-preview");null!==t&&null!==t.parentNode&&t.parentNode.removeChild(t)}_paintSelectionRect(t,e){let i=Math.min(t.x,e.x),s=Math.min(t.y,e.y),n=Math.abs(t.x-e.x),r=Math.abs(t.y-e.y);this._paintSelectionRectAt(i,s,n,r)}_paintSelectionRectFromRect(t){this._paintSelectionRectAt(t.x,t.y,t.width,t.height)}_paintSelectionRectAt(t,e,i,s){let n=this._svgRoot.querySelector(".hw-content");if(null===n)return;let r=n.querySelector(".hw-selection-rect");null===r&&(r=this._doc.createElementNS("http://www.w3.org/2000/svg","rect"),r.setAttribute("class","hw-selection-rect"),r.setAttribute("data-testid","selection-rect"),r.setAttribute("fill","rgba(31, 95, 205, 0.08)"),r.setAttribute("stroke","#1f5fcd"),r.setAttribute("stroke-width","1"),r.setAttribute("stroke-dasharray","4 3"),r.setAttribute("pointer-events","none"),n.appendChild(r)),r.setAttribute("x",String(t)),r.setAttribute("y",String(e)),r.setAttribute("width",String(i)),r.setAttribute("height",String(s))}_clearSelectionRect(){let t=this._svgRoot.querySelector(".hw-selection-rect");null!==t&&null!==t.parentNode&&t.parentNode.removeChild(t)}};Le._RDKIT_CACHE_LIMIT=256;function Oe(t){switch(t.kind){case"numeric":return`R${t.r}`;case"unspecified":return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${t.position}pos:R${t.r}`}}var Re=class t{constructor(t,e){this._onClose=null,this._primaryAction=null,this._host=t,this._doc=e.documentImpl??Ee(t);let i=this._doc,s={class:"hw-modal-backdrop",role:"presentation"};void 0!==e.testId&&(s["data-testid"]=`dialog-${e.testId}`);let n=Pe(i,"div",s),r={class:"hw-modal",role:"dialog","aria-modal":"true","aria-label":e.title};void 0!==e.testId&&(r["data-testid"]=`dialog-${e.testId}-frame`);let o=Pe(i,"div",r),l=Pe(i,"div",{class:"hw-modal__header"},[e.title]),a=Pe(i,"div",{class:"hw-modal__body"});o.appendChild(l),o.appendChild(a),n.appendChild(o);let c=t=>{t.stopPropagation()};for(let t of["mousedown","mousemove","mouseup","mouseover","mouseenter","mouseleave","wheel","contextmenu","dblclick","keydown","keyup","keypress"])n.addEventListener(t,c);o.addEventListener("keydown",t=>{let e=t;if("Enter"!==e.key||"TEXTAREA"===e.target?.tagName)return;let i=this._primaryAction;null!==i&&(e.preventDefault?.(),e.stopImmediatePropagation?.(),i())}),n.addEventListener("click",t=>{t.target!==n?t.stopPropagation():this.close()}),this.root=n,this.body=a}static anyOpen(){return t._openStack.length>0}static closeTopmost(){let e=t._openStack[t._openStack.length-1];return void 0!==e&&(e.close(),!0)}open(e){this._onClose=e??null,null===this.root.parentNode&&this._host.appendChild(this.root),t._openStack.includes(this)||t._openStack.push(this),Ne(this._doc)}close(){let e=t._openStack.indexOf(this);e>=0&&t._openStack.splice(e,1),null!==this.root.parentNode&&this.root.parentNode.removeChild(this.root);let i=this._onClose;this._onClose=null,null!==i&&i()}setPrimaryAction(t){this._primaryAction=t}get isOpen(){return null!==this.root.parentNode}};Re._openStack=[];Object.freeze(new Set);function Fe(t){return t.startsWith("[")&&t.endsWith("]")||1===t.length&&/^[A-Za-z]$/.test(t)?t:`[${t}]`}function De(t,e,i){return`${Fe(t)}(${Fe(e)})${Fe(i)}`}var He="http://www.w3.org/2000/svg",Be={sugar:At,base:Et,linker:Pt},Ge={sugar:["r","R"],base:["A"],linker:["p","P"]},Ve={x:70,y:60},Ue={x:140,y:60},We={x:70,y:130},Ye=class t{constructor(t,e,i){this.onValueSet=new Mt,this.onPickModeChange=new Mt,this._slots=new Map,this._favStar=null,this._pickMode=null,this._destroyed=!1,this._builderRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??Ee(t),this._hooks=i?.paletteHooks??null,this._favHooks=i?.favoriteHooks??null,this.element=Pe(this._doc,"div",{class:"hw-rna-builder","data-testid":"rna-builder"});let s=Pe(this._doc,"div",{class:"hw-rna-builder__header"});if(s.appendChild(Pe(this._doc,"div",{class:"hw-rna-builder__title"},["RNA builder"])),null!==this._favHooks){let t=Pe(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"},["☆"]),e=t=>{t.stopPropagation();let e=this.getSelection();""===e.preview||null===this._favHooks||this._favHooks.toggleFavoriteTriplet(e.sugar,e.base,e.linker)};t.addEventListener("click",e),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&e(t)}),this._favStar=t,s.appendChild(t)}this.element.appendChild(s),this._hintEl=Pe(this._doc,"div",{class:"hw-rna-builder__hint","data-testid":"rna-builder-hint",hidden:!0}),this.element.appendChild(this._hintEl);let n=this._buildSvg();this.element.appendChild(n),this._preview=Pe(this._doc,"div",{class:"hw-rna-builder__preview","data-testid":"rna-builder-preview"}),this.element.appendChild(this._preview),this._addBtn=Pe(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),t.appendChild(this.element);let r=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),o=e.on("theme:change",()=>{this._destroyed||this._repaintSlotColors()});this._libUnsub=()=>{try{r()}catch{}try{o()}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}getSelection(){let t=this._slots.get("sugar")?.value??"",e=this._slots.get("base")?.value??"",i=this._slots.get("linker")?.value??"";return{sugar:t,base:e,linker:i,preview:""!==t&&""!==e&&""!==i?De(t,e,i):""}}setField(t,e){let i=this._slots.get(t);void 0!==i&&(i.value=e,this._setLabelText(i.labelEl,e),this._repaintSlot(i),this._updatePreview(),this.onValueSet.next({field:t,symbol:e}))}startPickMode(t){this._pickMode!==t?(null!==this._pickMode&&this._setSlotPressed(this._pickMode,!1),this._pickMode=t,this._setSlotPressed(t,!0),this._setHintActive(t),this.onPickModeChange.next({field:t}),null!==this._hooks&&this._hooks.beginBiotypeFilter(Be[t],e=>{this.setField(t,e),this._exitPickMode()},()=>{this._exitPickMode()})):this.cancelPickMode()}cancelPickMode(){null!==this._pickMode&&(null!==this._hooks&&this._hooks.endBiotypeFilter(),this._exitPickMode())}getPickMode(){return this._pickMode}triggerAdd(){this._onAddClicked()}destroy(){this._destroyed||(this._destroyed=!0,null!==this._pickMode&&null!==this._hooks&&this._hooks.endBiotypeFilter(),this._libUnsub(),this.onValueSet.complete(),this.onPickModeChange.complete(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}_buildSvg(){let t=this._doc.createElementNS(He,"svg");t.setAttribute("class","hw-rna-builder__triplet"),t.setAttribute("viewBox","0 0 200 180"),t.setAttribute("data-testid","rna-builder-triplet-svg"),t.setAttribute("role","group"),t.setAttribute("aria-label","Triplet preview");let e=this._doc.createElementNS(He,"line");e.setAttribute("class","hw-rna-builder__bond"),e.setAttribute("x1",String(Ve.x+18)),e.setAttribute("y1",String(Ve.y)),e.setAttribute("x2",String(Ue.x-18)),e.setAttribute("y2",String(Ue.y)),t.appendChild(e);let i=this._doc.createElementNS(He,"line");i.setAttribute("class","hw-rna-builder__bond"),i.setAttribute("x1",String(Ve.x)),i.setAttribute("y1",String(Ve.y+18)),i.setAttribute("x2",String(We.x)),i.setAttribute("y2",String(We.y-22)),t.appendChild(i);let s=this._doc.createElementNS(He,"rect");s.setAttribute("class","hw-rna-builder__slot-shape"),s.setAttribute("x",String(-18)),s.setAttribute("y",String(-18)),s.setAttribute("width",String(36)),s.setAttribute("height",String(36)),s.setAttribute("rx","8"),s.setAttribute("ry","8");let n=this._buildSlot("sugar","Pick sugar (backbone)",Ve,s),r=this._doc.createElementNS(He,"circle");r.setAttribute("class","hw-rna-builder__slot-shape"),r.setAttribute("cx","0"),r.setAttribute("cy","0"),r.setAttribute("r",String(18));let o=this._buildSlot("linker","Pick linker",Ue,r),l=this._doc.createElementNS(He,"path");l.setAttribute("class","hw-rna-builder__slot-shape"),l.setAttribute("d","M -22 0 L 0 -22 L 22 0 L 0 22 Z");let a=this._buildSlot("base","Pick base",We,l);return t.appendChild(o.groupEl),t.appendChild(n.groupEl),t.appendChild(a.groupEl),this._slots.set("sugar",n),this._slots.set("linker",o),this._slots.set("base",a),t}_buildSlot(t,e,i,s){let n=this._doc.createElementNS(He,"g");n.setAttribute("class","hw-rna-builder__slot"),n.setAttribute("data-slot",t),n.setAttribute("data-testid",`rna-builder-slot-${t}`),n.setAttribute("role","button"),n.setAttribute("tabindex","0"),n.setAttribute("aria-label",e),n.setAttribute("aria-pressed","false"),n.setAttribute("transform",`translate(${i.x} ${i.y})`),n.appendChild(s);let r=this._doc.createElementNS(He,"text");r.setAttribute("class","hw-rna-builder__slot-label"),r.setAttribute("data-testid",`rna-builder-${t}-value`),r.setAttribute("x","0"),r.setAttribute("y","0"),r.setAttribute("text-anchor","middle"),r.setAttribute("dominant-baseline","central"),n.appendChild(r);let o=e=>{e.stopPropagation(),this.startPickMode(t)};return n.addEventListener("click",o),n.addEventListener("keydown",t=>{let e=t;("Enter"===e.key||" "===e.key)&&o(t)}),n.addEventListener("mouseenter",e=>this._showSlotTooltip(t,e)),n.addEventListener("mouseleave",()=>this._hideSlotTooltip()),n.addEventListener("focus",()=>this._showSlotTooltip(t,null)),n.addEventListener("blur",()=>this._hideSlotTooltip()),{id:t,biotype:Be[t],groupEl:n,shapeEl:s,labelEl:r,value:""}}_setLabelText(t,e){let i=[];for(let e=t.firstChild;null!==e;e=e.nextSibling)"title"===e.nodeName||"TITLE"===e.nodeName||i.push(e);for(let e of i)t.removeChild(e);let s=function(t){let e=t.length;return e<=2?16:e<=4?11:e<=7?8:e<=10?6:5}(e);t.setAttribute("font-size",String(s)),t.setAttribute("text-anchor","middle"),t.setAttribute("dominant-baseline","central");let n=e.length>10?`${e.slice(0,9)}…`:e;t.appendChild(this._doc.createTextNode(n));let r=t.parentNode;if(null!==r){let t=null;for(let e=r.firstChild;null!==e;e=e.nextSibling)if("title"===e.nodeName||"TITLE"===e.nodeName){t=e;break}for(null===t&&(t=this._doc.createElementNS(He,"title"),r.insertBefore(t,r.firstChild));null!==t.firstChild;)t.removeChild(t.firstChild);t.appendChild(this._doc.createTextNode(e))}}_repaintSlotColors(){for(let t of this._slots.values())this._repaintSlot(t)}_repaintSlot(t){let e=this._editor.getService().monomerLib,i=this._theme(),s=""===t.value?null:function(t,e,i){return t.getMonomerSet(e).get(i)??null}(e,t.biotype,t.value),n=ie(s,t.biotype,i.colorTheme);t.shapeEl.style.fill=n.background,t.shapeEl.style.stroke=n.line,t.labelEl.style.fill=n.text}_populateDefaults(){let t=this._editor.getService().monomerLib;for(let[e,i]of this._slots.entries()){let s=qe(t,i.biotype),n=Ke(s,Ge[e]),r=""!==i.value&&s.some(t=>t.symbol===i.value)?i.value:n??s[0]?.symbol??"";i.value=r,this._setLabelText(i.labelEl,r)}}_updatePreview(){let t=this.getSelection();for(;null!==this._preview.firstChild;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(""===t.preview?"-":t.preview)),this._updateFavStar(t)}_updateFavStar(t){if(null===this._favStar||null===this._favHooks)return;let e=""!==t.preview,i=e&&this._favHooks.isFavoriteTriplet(t.sugar,t.base,t.linker);for(;null!==this._favStar.firstChild;)this._favStar.removeChild(this._favStar.firstChild);this._favStar.appendChild(this._doc.createTextNode(i?"★":"☆")),this._favStar.setAttribute("aria-pressed",i?"true":"false"),e?this._favStar.removeAttribute("aria-disabled"):this._favStar.setAttribute("aria-disabled","true");let s="hw-rna-builder__fav"+(i?" hw-rna-builder__fav--active":"")+(e?"":" hw-rna-builder__fav--disabled");this._favStar.setAttribute("class",s)}_onAddClicked(){let t=this.getSelection();""!==t.preview&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)}_exitPickMode(){if(null===this._pickMode)return;let t=this._pickMode;this._setSlotPressed(t,!1),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null})}_setHintActive(t){let e=this._hintEl;for(;null!==e.firstChild;)e.removeChild(e.firstChild);if(null===t)return void e.setAttribute("hidden","");e.removeAttribute("hidden");let i="sugar"===t?"sugar":"base"===t?"base":"linker";e.appendChild(this._doc.createTextNode(`Pick ${i} from palette`))}_setSlotPressed(t,e){let i=this._slots.get(t);if(void 0===i)return;i.groupEl.setAttribute("aria-pressed",e?"true":"false");let s=(i.groupEl.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-rna-builder__slot--active"!==t).join(" ");i.groupEl.setAttribute("class",e?`${s} hw-rna-builder__slot--active`:s)}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_builderRdkitSvgFor(e){if(null===e)return null;let i=e.smiles;if(void 0===i||""===i)return null;let s=this._rdkit();if(null===s)return null;let n=`${e.polymerType}:${e.symbol}`;if(this._builderRdkitCache.has(n))return this._builderRdkitCache.get(n)??null;let r=ke(s,i,220,140);if(this._builderRdkitCache.size>=t._BUILDER_RDKIT_CACHE_LIMIT){let t=this._builderRdkitCache.keys().next().value;void 0!==t&&this._builderRdkitCache.delete(t)}return this._builderRdkitCache.set(n,r),r}_slotHint(t){switch(t){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(t,e){let i=""===e?"?":e;switch(t){case"sugar":return`Sugar: ${i}`;case"base":return`Base: ${i}`;case"linker":return`Linker: ${i}`}}_showSlotTooltip(t,e){let i=this._slots.get(t);if(void 0===i)return;let s=this._editor.getService().monomerLib.getMonomerSet(i.biotype),n=""===i.value?null:s.get(i.value)??null,r=Se(this._doc,"builder-tooltip","hw-builder-tooltip");$e(this._doc,r,{symbol:this._slotTitle(t,i.value),name:n?.name??"",rdkitSvg:this._builderRdkitSvgFor(n),rdkitTestid:"builder-tooltip-rdkit-svg",hint:this._slotHint(t)});let o=e;if(null!==o&&"number"==typeof o.clientX&&"number"==typeof o.clientY)Ie(r,o.clientX,o.clientY);else{let t=i.groupEl,e="function"==typeof t.getBoundingClientRect?t.getBoundingClientRect():null;null!==e?Ie(r,e.left+e.width/2,e.top+e.height/2):Ie(r,0,0)}}_hideSlotTooltip(){Me(this._doc.body.querySelector('[data-testid="builder-tooltip"]'))}};Ye._BUILDER_RDKIT_CACHE_LIMIT=256;var ze=Ye;function qe(t,e){let i=t.getMonomerSet(e),s=[];for(let t of i.values())s.push(t);return s.sort((t,e)=>t.symbol.localeCompare(e.symbol)),s}function Ke(t,e){let i=new Set;for(let e of t)i.add(e.symbol);for(let t of e)if(i.has(t))return t;return null}var je="Favorites",Qe={[je]:"★ Favorites",[It.PEPTIDE]:"Peptides",[It.RNA]:"RNA",[It.CHEM]:"CHEM",[It.BLOB]:"BLOB",G:"G"},Xe=[je,It.PEPTIDE,It.RNA,It.CHEM,It.BLOB,"G"],Je="hwe:palette:favorites",Ze="hwe:palette:active-tab";function ti(t){return`${t.sugar}|${t.base}|${t.linker}`}var ei=class t{constructor(t,e,i){this.favoritesChanged=new Mt,this._nextAddUnsub=()=>{},this._favorites=new Set,this._favoriteTriplets=[],this._pendingRnaSelection=null,this._visibleTabs=[je],this._activeTab=je,this._searchInput=null,this._filter="",this._destroyed=!1,this._rnaBuilder=null,this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,this._pickEscapeListener=null,this._pickOutsideClickListener=null,this._paletteRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??Ee(t),this._opts={documentImpl:this._doc,groupByNaturalAnalog:i?.groupByNaturalAnalog??!0,allowFavorites:i?.allowFavorites??!0},this._loadFavorites(),this._activeTab=this._resolveInitialTab(i?.initialTab),this.element=Pe(this._doc,"div",{class:"hw-palette","data-testid":"palette"}),t.appendChild(this.element),this._render(),this._libUnsub=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),this._themeUnsub=e.on("theme:change",()=>{this._destroyed||this.refresh()}),this._nextAddUnsub=e.on("option:change",t=>{this._destroyed||"nextAdd"===t.key&&this._updatePrimedClasses()})}refresh(){this._render()}setFilter(t){this._filter=t.trim().toLowerCase(),null!==this._searchInput&&this._searchInput.value!==t&&(this._searchInput.value=t),this._applyFilter()}setActiveTab(t){this._visibleTabs.includes(t)&&(this._activeTab=t,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter())}getActiveTab(){return this._activeTab}getFavorites(){let t=this._editor.getService().monomerLib,e=[];for(let i of this._favorites)null!==this._findMonomer(t,i)&&e.push(i);return e}setFavorite(t,e){e!==this._favorites.has(t)&&(e?this._favorites.add(t):this._favorites.delete(t),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}clearFavorites(){0===this._favorites.size&&0===this._favoriteTriplets.length||(this._favorites.clear(),this._favoriteTriplets.length=0,this._saveFavorites(),this._render(),this._emitFavoritesChanged())}getFavoriteTriplets(){return this._favoriteTriplets.map(t=>({...t}))}isFavoriteTriplet(t,e,i){let s=ti({sugar:t,base:e,linker:i});return this._favoriteTriplets.some(t=>ti(t)===s)}setFavoriteTriplet(t,e,i,s){let n=ti({sugar:t,base:e,linker:i}),r=this._favoriteTriplets.findIndex(t=>ti(t)===n);s!==r>=0&&(s?this._favoriteTriplets.push({sugar:t,base:e,linker:i}):this._favoriteTriplets.splice(r,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}_hidePaletteTooltips(){let t=this._doc.body;Me(t.querySelector('[data-testid="palette-tooltip"]')),Me(t.querySelector('[data-testid="palette-triplet-tooltip"]'))}_emitFavoritesChanged(){this.favoritesChanged.next({favorites:this.getFavorites(),triplets:this.getFavoriteTriplets()})}destroy(){this._destroyed||(this._destroyed=!0,null!==this._rnaBuilder&&(this._rnaBuilder.destroy(),this._rnaBuilder=null),this._libUnsub(),this._themeUnsub(),this._nextAddUnsub(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}getRnaBuilder(){return this._rnaBuilder}hasActiveBiotypeFilter(){return null!==this._activeBiotypeFilter}getActiveBiotypeFilter(){return this._activeBiotypeFilter}cancelBiotypeFilter(){if(null===this._activeBiotypeFilter)return;let t=this._pickCanceller;this._teardownPickMode(),t?.()}_buildPaletteFilterHooks(){return{beginBiotypeFilter:(t,e,i)=>{null!==this._activeBiotypeFilter&&this._teardownPickMode(),this._activeBiotypeFilter=t,this._pickResolver=e,this._pickCanceller=i,this._applyFilter();let s=t=>{"Escape"===t.key&&this.cancelBiotypeFilter()};this._pickEscapeListener=s,this._doc.defaultView?.addEventListener("keydown",s);let n=t=>{if(null===this._activeBiotypeFilter)return;let e=t.target;if(null==e)return;let i=this._activeBiotypeFilter,s=e;for(;null!==s;){let t=void 0===s.getAttribute?null:s.getAttribute("class");if(null!==t){let e=t.split(/\s+/);if(e.includes("hw-palette__tile")){if((s.getAttribute("data-biotype")??"")===i)return;break}if(e.includes("hw-rna-builder__slot")){if(this._isInsideOwnPalette(s))return;break}}s=s.parentElement}this.cancelBiotypeFilter()};this._pickOutsideClickListener=n,this._doc.addEventListener("mousedown",n,!0)},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let t=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`);if(null===t)return;let e=t;try{if("function"==typeof e.scrollTo)return void e.scrollTo({top:0,behavior:"smooth"})}catch{}"number"==typeof e.scrollTop&&(e.scrollTop=0)}_isInsideOwnPalette(t){let e=t;for(;null!==e;){if(e===this.element)return!0;e=e.parentElement}return!1}_teardownPickMode(){null!==this._activeBiotypeFilter&&(this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,null!==this._pickEscapeListener&&(this._doc.defaultView?.removeEventListener("keydown",this._pickEscapeListener),this._pickEscapeListener=null),null!==this._pickOutsideClickListener&&(this._doc.removeEventListener("mousedown",this._pickOutsideClickListener,!0),this._pickOutsideClickListener=null),this._applyFilter())}_render(){for(null!==this._rnaBuilder&&(this._pendingRnaSelection=this._rnaBuilder.getSelection(),this._rnaBuilder.destroy(),this._rnaBuilder=null);null!==this.element.firstChild;)this.element.removeChild(this.element.firstChild);let t=this._doc.createElement("input");t.setAttribute("type","search"),t.setAttribute("class","hw-palette__search"),t.setAttribute("placeholder","Search monomers..."),t.setAttribute("data-testid","palette-search"),""!==this._filter&&(t.value=this._filter),t.addEventListener("input",()=>this.setFilter(t.value)),this._searchInput=t,this.element.appendChild(t),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=je);let e=Pe(this._doc,"div",{class:"hw-palette__tabs",role:"tablist","data-testid":"palette-tabs"});for(let t of this._visibleTabs){let i=t===this._activeTab,s=Pe(this._doc,"button",{class:"hw-palette__tab",type:"button",role:"tab","aria-controls":`hw-palette-pane-${t}`,"aria-selected":i?"true":"false","data-testid":`palette-tab-${t}`,"data-tab":t,title:Qe[t]},[Qe[t]]);s.addEventListener("click",()=>this.setActiveTab(t)),e.appendChild(s)}this.element.appendChild(e);let i=Pe(this._doc,"div",{class:"hw-palette__panes"}),s=this._theme(),n=this._editor.getService().monomerLib;for(let t of this._visibleTabs){let e=t===this._activeTab,r=Pe(this._doc,"div",{class:"hw-palette__pane",id:`hw-palette-pane-${t}`,role:"tabpanel","data-testid":`palette-pane-${t}`,"data-tab":t,hidden:!e});t===je?this._buildFavoritesPane(r,n,s):this._buildPolymerPane(r,t,n,s),i.appendChild(r)}this.element.appendChild(i),this._applyFilter()}_computeVisibleTabs(){let t=this._editor.getService().monomerLib,e=new Set;for(let i of t.getPolymerTypes())e.add(i);let i=[];i.push(je);for(let t of Xe)t!==je&&e.has(t)&&i.push(t);return i}_buildFavoritesPane(t,e,i){let s=this._resolveFavoriteMonomers(e),n=this._favoriteTriplets;if(0===s.length&&0===n.length){let e=Pe(this._doc,"div",{class:"hw-palette__placeholder","data-testid":"palette-favorites-empty"},["No favorites yet — click the ☆ on any tile to add one."]);return void t.appendChild(e)}for(let[e,i]of this._groupByPolymerAndType(s))t.appendChild(this._renderGroup(e,i));n.length>0&&t.appendChild(this._renderTripletGroup("RNA · Triplets",n,e))}_groupByPolymerAndType(t){let e=new Map;for(let i of t){let t=i.polymerType,s=i.monomerType??"Undefined",n=`${t}|${s}`,r=e.get(n);void 0===r&&(r={pt:t,mt:s,list:[]},e.set(n,r)),r.list.push(i)}let i=t=>{let e=Xe.indexOf(t);return e<0?99:e},s={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(e.values()).sort((t,e)=>i(t.pt)-i(e.pt)||(s[t.mt]??9)-(s[e.mt]??9)||t.mt.localeCompare(e.mt)).map(t=>[`${this._polymerLabel(t.pt)} · ${t.mt}`,t.list])}_polymerLabel(t){return Qe[t]??t}_renderTripletGroup(t,e,i){let s=Pe(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),n=Pe(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),r=Pe(this._doc,"div",{class:"hw-triplet-chips","data-testid":"palette-triplet-favorites"});for(let t of e)r.appendChild(this._renderTripletChip(t,i));return s.appendChild(n),s.appendChild(r),s}_renderTripletChip(t,e){let i=De(t.sugar,t.base,t.linker),s=e.getMonomerSet(Et).get(t.base)??null,n=ie(s,Et,this._theme().colorTheme),r=this.isFavoriteTriplet(t.sugar,t.base,t.linker),o=void 0!==s?.name&&""!==s.name?`${i} — ${s.name}`:i,{root:l}=function(t,e){let i=!1!==e.showStar,s=Pe(t,"span",{class:"hw-triplet-chip__star"},[e.favorite?"★":"☆"]),n=Pe(t,"span",{class:"hw-triplet-chip__label"},[e.label]),r=["hw-triplet-chip"];e.favorite&&r.push("hw-triplet-chip--favorite");let o=i?[s,n]:[n];return{root:Pe(t,"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};`},o),star:s}}(this._doc,{sugar:t.sugar,base:t.base,linker:t.linker,label:i,title:o,background:Gt(n.background),textColor:n.text,favorite:r,showStar:this._opts.allowFavorites});return this._wireTripletChip(l,t),l}_wireTripletChip(t,e){t.addEventListener("mouseenter",t=>{let i=t,s=Se(this._doc,"palette-triplet-tooltip","hw-palette-tooltip hw-triplet-tooltip");(function(t,e,i){for(;null!==e.firstChild;)e.removeChild(e.firstChild);e.appendChild(Pe(t,"div",{class:"hw-tooltip__symbol"},[i.title]));let s=Pe(t,"div",{class:"hw-tooltip__triplet"});for(let e of i.parts){let n=Pe(t,"div",{class:"hw-tooltip__triplet-part"});if(n.appendChild(Pe(t,"div",{class:"hw-tooltip__triplet-role"},[`${e.role}: ${e.symbol}`])),void 0!==e.name&&""!==e.name&&e.name!==e.symbol&&n.appendChild(Pe(t,"div",{class:"hw-tooltip__name"},[e.name])),void 0!==e.rdkitSvg&&null!==e.rdkitSvg&&""!==e.rdkitSvg){let s={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(s["data-testid"]=i.rdkitTestid);let r=Pe(t,"div",s);r.innerHTML=e.rdkitSvg,n.appendChild(r)}s.appendChild(n)}e.appendChild(s),void 0!==i.hint&&""!==i.hint&&e.appendChild(Pe(t,"div",{class:"hw-tooltip__hint"},[i.hint]))})(this._doc,s,{title:De(e.sugar,e.base,e.linker),parts:this._tripletTooltipParts(e),hint:"Click to add this triplet",rdkitTestid:"palette-triplet-tooltip-rdkit-svg"}),Ie(s,"number"==typeof i.clientX?i.clientX:0,"number"==typeof i.clientY?i.clientY:0)}),t.addEventListener("mouseleave",()=>{Me(this._doc.body.querySelector('[data-testid="palette-triplet-tooltip"]'))}),t.addEventListener("click",t=>{let i=t.target;if(this._opts.allowFavorites&&!0===i?.classList?.contains("hw-triplet-chip__star"))return this.setFavoriteTriplet(e.sugar,e.base,e.linker,!this.isFavoriteTriplet(e.sugar,e.base,e.linker)),void t.stopPropagation();this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)}),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)})}_buildRnaDefaultChips(e){let i=this._pickSymbol(e.getMonomerSet(At),["r","R"]),s=this._pickSymbol(e.getMonomerSet(Pt),["p","P"]),n=e.getMonomerSet(Et);if(null===i||null===s)return null;let r=t._DEFAULT_TRIPLET_BASES.filter(t=>n.has(t));if(0===r.length)return null;let o=Pe(this._doc,"div",{class:"hw-triplet-chips hw-triplet-chips--defaults","data-testid":"rna-default-triplets"});for(let t of r)o.appendChild(this._renderTripletChip({sugar:i,base:t,linker:s},e));return o}_tripletTooltipParts(t){let e=this._editor.getService().monomerLib,i=(t,i,s)=>{let n=e.getMonomerSet(i).get(s)??null;return{role:t,symbol:s,...void 0!==n?.name?{name:n.name}:{},rdkitSvg:null===n?null:this._paletteRdkitSvg(n)}};return[i("Sugar",At,t.sugar),i("Base",Et,t.base),i("Linker",Pt,t.linker)]}_pickSymbol(t,e){for(let i of e)if(t.has(i))return i;let i=t.keys().next();return!0===i.done?null:i.value}_restoreRnaSelection(){let t=this._pendingRnaSelection;if(this._pendingRnaSelection=null,null===t||null===this._rnaBuilder)return;let e=this._editor.getService().monomerLib;""!==t.sugar&&e.getMonomerSet(At).has(t.sugar)&&this._rnaBuilder.setField("sugar",t.sugar),""!==t.base&&e.getMonomerSet(Et).has(t.base)&&this._rnaBuilder.setField("base",t.base),""!==t.linker&&e.getMonomerSet(Pt).has(t.linker)&&this._rnaBuilder.setField("linker",t.linker)}_resolveFavoriteMonomers(t){let e=[];for(let i of this._favorites){let s=this._findMonomer(t,i);null!==s&&e.push(s)}return e}_findMonomer(t,e){for(let i of t.getPolymerTypes()){let s=t.getMonomer(i,e);if(null!==s)return s}return null}_buildPolymerPane(t,e,i,s){let n=e,r=this._monomersForPolymer(n,i);if(0===r.length)return;if(n===It.RNA){this._rnaBuilder=new ze(t,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(t,e,i)=>this.isFavoriteTriplet(t,e,i),toggleFavoriteTriplet:(t,e,i)=>this.setFavoriteTriplet(t,e,i,!this.isFavoriteTriplet(t,e,i))}:null}),this._restoreRnaSelection();let e=this._buildRnaDefaultChips(i);null!==e&&t.appendChild(e);let s=this._groupRna(r);for(let[e,i]of s)0!==i.length&&t.appendChild(this._renderGroup(e,i));return}if(n===It.PEPTIDE&&this._opts.groupByNaturalAnalog){let e=this._groupByAnalog(r);for(let[i,s]of e){let e=""===i?"Other":i;t.appendChild(this._renderGroup(e,s))}return}let o=Pe(this._doc,"div",{class:"hw-palette__group-tiles"}),l=this._editor.getNextAddSymbol(),a=this._sortByColor(r);for(let t of a){let e=this._biotype(t,n);o.appendChild(this._renderTile(t,e,l))}t.appendChild(o)}_renderGroup(t,e){let i=Pe(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),s=Pe(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),n=Pe(this._doc,"div",{class:"hw-palette__group-tiles"}),r=this._editor.getNextAddSymbol(),o=this._sortByColor(e);for(let t of o){let e=this._biotype(t,t.polymerType);n.appendChild(this._renderTile(t,e,r))}return i.appendChild(s),i.appendChild(n),i}_sortByColor(t){let e=this._theme(),i=t.map((t,i)=>{let s=function(t){let e=Ot(t);if(null===e)return{h:0,s:0,l:0};let[i,s,n]=Dt(e[0],e[1],e[2]);return{h:i,s,l:n}}(ie(t,this._biotype(t,t.polymerType),e.colorTheme).background),n=0===s.s?1:0;return{m:t,idx:i,h:s.h,s:s.s,l:s.l,isGrey:n}});return i.sort((t,e)=>t.isGrey!==e.isGrey?t.isGrey-e.isGrey:t.h!==e.h?t.h-e.h:t.s!==e.s?t.s-e.s:t.l!==e.l?t.l-e.l:t.idx-e.idx),i.map(t=>t.m)}_monomersForPolymer(t,e){let i=e.getMonomerSymbolsByType(t),s=[];for(let n of i){let i=e.getMonomer(t,n);null!==i&&s.push(i)}return s.sort((t,e)=>t.symbol.localeCompare(e.symbol)),s}_groupByAnalog(t){let e=new Map;for(let i of t){let t=i.naturalAnalog??"",s=e.get(t);void 0===s&&(s=[],e.set(t,s)),s.push(i)}let i=[],s=Array.from(e.keys()).sort((t,e)=>""===t&&""!==e?1:""===e&&""!==t?-1:t.localeCompare(e));for(let t of s)i.push([t,e.get(t)]);return new Map(i)}_groupRna(t){let e=[],i=[],s=[],n=[];for(let r of t){let t=se(r);t===At?e.push(r):t===Et?i.push(r):t===Pt?s.push(r):n.push(r)}let r=new Map;return r.set("Backbones",e),r.set("Bases",i),r.set("Linkers",s),n.length>0&&r.set("Other",n),r}_renderTile(t,e,i){let s=this._favorites.has(t.symbol),n=null!==i&&i.symbol===t.symbol&&i.biotype===e,{root:r,star:o}=function(t,e){let i=ie(e.monomer,e.biotype,e.theme.colorTheme),s=Gt(i.background),n=i.text,r=function(t,e){let i=Vt(t),s=Vt(e);return(Math.max(i,s)+.05)/(Math.min(i,s)+.05)}(n,s)<5,o=e.monomer.symbol,l=function(t){return t<=3?14:t<=6?11:t<=9?9:8}(o.length),a=`font-size:${l}px;${o.length>=10?"line-height:1.1;letter-spacing:-0.02em;":""}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:80px;display:inline-block;`,c=Pe(t,"span",{class:"hw-palette__star"},[e.favorite?"★":"☆"]),h=Pe(t,"span",{class:"hw-palette__label",style:a},[o]),d=["hw-palette__tile"];e.primed&&d.push("hw-palette__tile--primed"),e.favorite&&d.push("hw-palette__tile--favorite"),r&&d.push("hw-palette__tile--low-contrast");let u=void 0!==e.monomer.name?`${o} — ${e.monomer.name}`:o,p=`background:${s};color:${n};width:100%;min-width:48px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return{root:Pe(t,"div",{class:d.join(" "),draggable:"true",role:"button","aria-pressed":e.primed?"true":"false","aria-label":u,"data-symbol":o,"data-biotype":e.biotype,"data-bg":s,"data-raw-bg":i.background,"data-testid":`palette-tile-${o}`,title:u,style:p},[c,h]),star:c}}(this._doc,{monomer:t,biotype:e,theme:this._theme(),favorite:s,primed:n});return this._wireTile(r,o,t,e),r}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_paletteRdkitSvg(e){let i=e.smiles;if(void 0===i||""===i)return null;let s=this._rdkit();if(null===s)return null;let n=`${e.polymerType}:${e.symbol}`;if(this._paletteRdkitCache.has(n))return this._paletteRdkitCache.get(n)??null;let r=ke(s,i,220,140);if(this._paletteRdkitCache.size>=t._PALETTE_RDKIT_CACHE_LIMIT){let t=this._paletteRdkitCache.keys().next().value;void 0!==t&&this._paletteRdkitCache.delete(t)}return this._paletteRdkitCache.set(n,r),r}_wireTile(t,e,i,s){t.addEventListener("mouseenter",t=>{let e=t,s=Se(this._doc,"palette-tooltip","hw-palette-tooltip");$e(this._doc,s,{symbol:i.symbol,name:i.name??"",rdkitSvg:this._paletteRdkitSvg(i),rdkitTestid:"palette-tooltip-rdkit-svg"}),Ie(s,"number"==typeof e.clientX?e.clientX:0,"number"==typeof e.clientY?e.clientY:0)}),t.addEventListener("mouseleave",()=>{Me(this._doc.body.querySelector('[data-testid="palette-tooltip"]'))}),t.addEventListener("click",t=>{let e=t.target;if(this._opts.allowFavorites&&void 0!==e&&!0===e?.classList?.contains("hw-palette__star"))return this.setFavorite(i.symbol,!this._favorites.has(i.symbol)),void t.stopPropagation();if(null!==this._activeBiotypeFilter&&this._activeBiotypeFilter===s){let e=this._pickResolver;return this._teardownPickMode(),e?.(i.symbol),this._scrollActivePaneToTop(),void t.stopPropagation()}let n=this._editor.getSelection();if(n.atoms.size>0){let e=this._editor.getMol(),r=[];for(let t of n.atoms){let i=e.atoms.find(e=>e.id===t);void 0!==i&&r.push(i)}return r.length>0&&r.every(t=>t.biotype===s)?(this._editor.replaceMonomers(r,i.symbol),void t.stopPropagation()):(this._editor.fire("editor:status",{message:`Cannot bulk-replace ${r.length} selected atom(s) with ${i.symbol}: selection contains incompatible biotypes for ${s}.`,severity:"warn",durationMs:3e3}),void t.stopPropagation())}let r=this._editor.getNextAddSymbol();if(null!==r&&r.symbol===i.symbol&&r.biotype===s)return this._editor.setNextAddSymbol(null),void this._updatePrimedClasses();this._editor.setNextAddSymbol(i.symbol,s),this._updatePrimedClasses()}),t.addEventListener("dragstart",t=>{let e=t.dataTransfer;if(null!=e)try{e.setData("application/x-hwe-monomer",JSON.stringify({symbol:i.symbol,biotype:s})),e.effectAllowed="copy"}catch{}Me(this._doc.body.querySelector('[data-testid="palette-tooltip"]')),this._editor.startPaletteDrag(i.symbol,s)})}_biotype(t,e){let i=se(t);if(null!==i)return i;switch(e){case It.PEPTIDE:return xt;case It.RNA:return At;case It.CHEM:return kt;case It.BLOB:return St;default:return kt}}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_applyFilter(){let t=this._filter,e=this._activeBiotypeFilter,i=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`),s=(i??this.element).querySelectorAll(".hw-palette__tile");for(let i=0;i<s.length;i++){let n=s[i],r=(n.getAttribute("data-symbol")??"").toLowerCase(),o=(n.getAttribute("title")??"").toLowerCase(),l=n.getAttribute("data-biotype")??"",a=(""===t||r.indexOf(t)>=0||o.indexOf(t)>=0)&&(null===e||l===e);n.style.display=a?"":"none"}let n=(i??this.element).querySelectorAll(".hw-triplet-chip");for(let i=0;i<n.length;i++){let s=n[i],r=[s.getAttribute("data-triplet")??"",s.getAttribute("data-sugar")??"",s.getAttribute("data-base")??"",s.getAttribute("data-linker")??""].join(" ").toLowerCase(),o=(""===t||r.indexOf(t)>=0)&&null===e;s.style.display=o?"":"none"}let r=(i??this.element).querySelectorAll(".hw-palette__group");for(let t=0;t<r.length;t++){let e=r[t],i=e.querySelectorAll(".hw-palette__tile, .hw-triplet-chip"),s=!1;for(let t=0;t<i.length;t++)if("none"!==i[t].style.display){s=!0;break}s?(e.removeAttribute("hidden"),e.removeAttribute("data-section-empty")):(e.setAttribute("hidden",""),e.setAttribute("data-section-empty","true"))}}_updatePrimedClasses(){let t=this._editor.getNextAddSymbol(),e=this.element.querySelectorAll(".hw-palette__tile");for(let i=0;i<e.length;i++){let s=e[i],n=s.getAttribute("data-symbol")??"",r=s.getAttribute("data-biotype")??"",o=null!==t&&t.symbol===n&&t.biotype===r,l=(s.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-palette__tile--primed"!==t).join(" ");s.setAttribute("class",o?`${l} hw-palette__tile--primed`:l),s.setAttribute("aria-pressed",o?"true":"false")}}_applyActiveTabClasses(){let t=this.element.querySelectorAll(".hw-palette__tab");for(let e=0;e<t.length;e++){let i=t[e],s=i.getAttribute("data-tab")??"";i.setAttribute("aria-selected",s===this._activeTab?"true":"false")}let e=this.element.querySelectorAll(".hw-palette__pane");for(let t=0;t<e.length;t++){let i=e[t];(i.getAttribute("data-tab")??"")===this._activeTab?i.removeAttribute("hidden"):i.setAttribute("hidden","")}}_localStorage(){if(!this._opts.allowFavorites)return null;let t=this._doc.defaultView;if(null==t)return null;try{return t.localStorage??null}catch{return null}}_resolveInitialTab(t){if(void 0!==t&&Xe.includes(t))return t;let e=this._localStorage();if(null!==e)try{let t=e.getItem(Ze);if(null!==t&&Xe.includes(t))return t}catch{}return je}_persistActiveTab(){let t=this._localStorage();if(null!==t)try{t.setItem(Ze,this._activeTab)}catch{}}_loadFavorites(){let t=this._localStorage();if(null!==t){try{let e=t.getItem(Je);if(null!==e&&""!==e){let t=JSON.parse(e),i=this._extractSymbols(t);for(let t of i)this._favorites.add(t);for(let e of this._extractTriplets(t))this._favoriteTriplets.push(e);return}}catch{}try{let e=t.getItem("hwe.palette.favorites");if(null===e||""===e)return;let i=JSON.parse(e);if(Array.isArray(i)){for(let t of i){if("string"!=typeof t)continue;let e=t.indexOf("|"),i=e>=0?t.slice(e+1):t;""!==i&&this._favorites.add(i)}this._saveFavorites()}}catch{}}}_extractSymbols(t){if(Array.isArray(t)){let e=[];for(let i of t)"string"==typeof i&&e.push(i);return e}if(null!==t&&"object"==typeof t){let e=t;if(Array.isArray(e.symbols)){let t=[];for(let i of e.symbols)"string"==typeof i&&t.push(i);return t}}return[]}_extractTriplets(t){if(null===t||"object"!=typeof t)return[];let e=t;if(!Array.isArray(e.triplets))return[];let i=[];for(let t of e.triplets){if(null===t||"object"!=typeof t)continue;let e=t;"string"==typeof e.sugar&&"string"==typeof e.base&&"string"==typeof e.linker&&i.push({sugar:e.sugar,base:e.base,linker:e.linker})}return i}_saveFavorites(){let t=this._localStorage();if(null!==t)try{let e={symbols:Array.from(this._favorites)};this._favoriteTriplets.length>0&&(e.triplets=this._favoriteTriplets.map(t=>({...t}))),t.setItem(Je,JSON.stringify(e))}catch{}}};ei._DEFAULT_TRIPLET_BASES=["A","C","G","U","T"],ei._PALETTE_RDKIT_CACHE_LIMIT=256;new Set([It.PEPTIDE,It.RNA,It.CHEM,It.BLOB]),new Set(["Backbone","Branch","Terminal","Undefined"]);var ii,si,ni;function ri(e,i=!0){if(null==e)return"rgb(100,100,100)";const s=t.Color.fromHtml(e);if(i){const e=t.Color.g(s),i=t.Color.r(s),n=t.Color.b(s),r=Math.sqrt(Math.pow(0-i,2)+Math.pow(0-e,2)+Math.pow(0-n,2));if(r>210)return`rgb(${i/r*210},${e/r*210},${n/r*210})`}return t.Color.toRgb(s)}!function(t){t[t.default=0]="default",t[t.continuous=1]="continuous"}(ii||(ii={})),function(t){t.Sequence="sequence",t.Helm="notation",t.Properties="properties",t.StructureView="structureview"}(si||(si={}));class oi{static hashCode(t){let e=0;if(0===t.length)return e;for(let i=0;i<t.length;i++)e=(e<<5)-e+t.charCodeAt(i),e|=0;return e}}class li{}class ai extends li{static get palette(){return ai._pallete||(ai._pallete=ai.buildPalette()),ai._pallete}static buildPalette(){return Z().then(t=>{t.awaitLoaded(1/0).then(()=>{const e=t.getMonomerLib();e.onChanged.subscribe(()=>{ai.customMonomerColors={},ai.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const i=e.getMonomerSymbolsByType(t);for(const s of i){const i=e.getMonomer(t,s);i?.meta?.colors?.default?.background&&(this.customMonomerColors[s]||(this.customMonomerColors[s]={}),this.customMonomerColors[s][t]=ri(i.meta.colors.default.background))}}})})}),[].concat(...Object.values(yt.colourPalette))}get(t,e){const i=ai.palette.length,s=ai.customMonomerColors[t],n=e??It.PEPTIDE;if(s&&s[n])return s[n];const r=oi.hashCode(t)%i;return ri(ai.palette[r])}}ai._pallete=null,ai.customMonomerColors={},ai.polymerTypes=[],P("renderers",()=>{let e,i;k(async()=>{await Q(),e=await Z(),i=await lt(),await e.loadMonomerLibForTests()}),S(async()=>{await at(i),await e.loadMonomerLib(!0)}),w("missedInLib",async()=>{await async function(){const e=await tt.dapi.files.readCsv("System:AppData/Helm/tests/sample_HELM-missedInLib.csv"),i=e.getCol("HELM"),s=tt.shell.addTableView(e);await F(()=>ht()(s.root).find(".d4-grid canvas").length>0,"Table view canvas not found",100),await tt.data.detectSemanticTypes(e),T(i.semType,t.SEMTYPE.MACROMOLECULE),T(i.meta.units,ut.HELM),T(i.getTag(t.TAGS.CELL_RENDERER),"helm");const n=i.getTag(".cell-renderer.render.error");if(n){const t=JSON.parse(n),e=new Error(t.message);throw e.stack=t.stack,e}}()}),w("scatterPlotTooltip",async()=>{await async function(){const e=t.DataFrame.fromCsv(s);e.currentRowIdx=0;const i=tt.shell.addTableView(e);await tt.data.detectSemanticTypes(e);const n=e.plot.scatter({x:"x",y:"y"});i.dockManager.dock(n,t.DOCK_TYPE.RIGHT,null),await Promise.all([v(n.onAfterDrawScene,()=>{},()=>{n.invalidateCanvas()},1e3),X(i.grid,500)]);const r=n.root.getBoundingClientRect(),o=n.worldToScreen(1,0),l=new MouseEvent("mousemove",{cancelable:!0,bubbles:!0,view:window,button:0,clientX:r.left+o.x,clientY:r.top+o.y}),a=ht()(n.root).find("canvas").get()[0];await v((0,dt.fromEvent)(a,"mousemove"),()=>{Ti.logger.debug(`Test: event, currentRowIdx=${e.currentRowIdx}`),T(ht()(K.tooltip.root).find("div table.d4-row-tooltip-table tr td canvas").length,1),T(n.hitTest(o.x,o.y),1)},()=>{a.dispatchEvent(l)},500),await X(i.grid,1e3)}()});const s="seq,x,y\nPEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$,0,0\nRNA1{r(A)p.r(C)p.r(G)p.r(U)p}$$$$,1,0\nRNA1{d(A)p.d(C)p.d(G)p.d(U)p}|PEPTIDE1{I.H.A.N.T.Thr_PO3H2}$$$$,0,1\n"}),function(t){t.TYPE="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t[t.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",t.RGP_LINE_START="M  RGP",t.ATOM_ALIAS_LINE_START="A  ",t.END="M  END"}(ni||(ni={}));class ci{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return null!==(t=this._atomTypes)&&void 0!==t||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let i=t;const s=this.isWhitespace(i)?e:e-1;for(let t=0;t<s;t++)i=this.getNextColumnIdx(i);return i}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let i=this.getAtomBlockIdx();for(let s=0;s<t;s++)i=this.shiftIdxToAtomType(i),e[s]=this.parseAtomType(i),i=this.getNextLineIdx(i);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),i=new Float32Array(this.atomCount);let s=this.getAtomBlockIdx();for(let n=0;n<this.atomCount;n++){s=this.shiftIdxToXColumn(s);for(const r of[t,e,i])r[n]=this.parseFloatValue(s),s=this.getNextColumnIdx(s);s=this.getNextLineIdx(s)}return{x:t,y:e,z:i}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let i=0;i<this.bondCount;i++){e=this.shiftIdxToBondedAtomsPair(e);const s=new Uint16Array(2);s[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),s[1]=this.parseIntValue(e),t[i]=s,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let i=this.getBondBlockIdx();for(let s=0;s<t;s++)i=this.shiftIdxToBondType(i),e[s]=this.parseIntValue(i),i=this.getNextLineIdx(i);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let i=e+1;for(;!this.isWhitespace(i);)++i;return t(this.fileContent.substring(e,i))}}class hi extends ci{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,i=e;return this.isQuote(e)?(i=this.getNextIdenticalChar(e),e++):i=this.fileContent.indexOf(" ",i),this.fileContent.substring(e,i)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment((t,e)=>{return 39===t||34===t||76===t&&!((i=this.fileContent.charCodeAt(e+1))>64&&i<91||i>96&&i<123);var i})}isFragment(){return this.isQueryOrFragment(t=>82===t||42===t)}isQueryOrFragment(t){const e=this.atomCount;let i=this.getAtomBlockIdx();for(let s=0;s<e;s++){if(i=this.shiftIdxToAtomType(i),t(this.fileContent.charCodeAt(i),i))return!0;i=this.getNextLineIdx(i)}return!1}}class di extends hi{constructor(t){super(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map,e=this.fileContent.split("\n");e.filter(t=>t.startsWith(ni.RGP_LINE_START)).forEach(e=>{const i=this.getAtomIdxToRgpIdxList(e);for(const[e,s]of i){if(t.has(e))throw new Error(`R group ${e} is already in the map`);t.set(e,s)}});const i=e.map((t,e)=>{if(t.startsWith(ni.ATOM_ALIAS_LINE_START))return e}).filter(t=>void 0!==t),s=i.map(t=>e[t]),n=i.map(t=>e[t+1]);s.forEach((e,i)=>{const s=parseInt(e.split(/\s+/)[1])-1,r=parseInt(n[i].substring(1));if(t.has(r))throw new Error(`R group ${r} is already in the map`);t.set(r,s)});const r=this.getRGroupAtomicIndices().filter(e=>!Array.from(t.values()).includes(e));if(0!==r.length)throw new Error(`Unaccounted R group indices: ${r}`);return t}getAtomIdxToRgpIdxList(t){const e=t.split(/\s+/).filter(t=>t).slice(3).map(t=>parseInt(t)),i=new Array(e.length/2);for(let t=0;t<e.length;t+=2)i[t/2]=[e[t+1],e[t]-1];return i}getRGroupAtomicIndices(){return this.atomTypes.map((t,e)=>{if(t.includes("R#"))return e}).filter(t=>void 0!==t)}static isValidMolfile(t){return-1!==t.indexOf(ni.TYPE)&&-1!==t.indexOf(ni.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,ni.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<ni.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,ni.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,ni.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+ni.NUM_OF_COUNTS_DIGITS;const i=parseInt(this.fileContent.substring(t,e));return t=e,e+=ni.NUM_OF_COUNTS_DIGITS,{atomCount:i,bondCount:parseInt(this.fileContent.substring(t,e))}}}class pi extends hi{constructor(t){super(t),this.init(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map;return this.getAtomLines().forEach((e,i)=>{const s=e.match(/RGROUPS=\(([\d\s]+)\)/);if(s){const e=s[1].split(/\s+/).map(t=>parseInt(t));if(e.length>2)throw new Error(`R group data ${e} has more than 2 elements`);const n=e[1];if(t.has(n))throw new Error(`R group ${n} is already in the map`);t.set(n,i)}}),t}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M  V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M  V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M  V30 BEGIN BOND"))}static isValidMolfile(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M  END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M  V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const i=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:i,bondCount:parseInt(this.fileContent.substring(t,e))}}}class fi{constructor(){}static getInstance(t){if(fi.isMolfileV2K(t))return new di(t);if(fi.isMolfileV3K(t))return new pi(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return di.isValidMolfile(t)}static isMolfileV3K(t){return pi.isValidMolfile(t)}}async function gi(){const e=t.Func.find({package:"Bio",name:"getSeqHelper"});if(0===e.length)throw new Error("Package 'Bio' must be installed for SeqHelper.");return(await e[0].prepare().call()).getOutputParamValue()}P("getMolfiles",()=>{let e,i;k(async()=>{await Q(),e=await Z(),i=await lt(),await e.loadMonomerLibForTests()}),S(async()=>{await at(i),await e.loadMonomerLib(!0)}),w("linear1",async()=>{const e=t.DataFrame.fromCsv("Helm, atoms, bonds\nPEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV}$$$$,11,10\nPEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV}$$$$,11,10\nPEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$,9,8"),i=e.getCol("Helm"),s=tt.shell.addTableView(e);Ti.logger.debug("Helm/getMolfiles/linear1, grid awaiting 1"),await X(s.grid,5e3),Ti.logger.debug("Helm/getMolfiles/linear1, grid awaited 1");const n=await tt.functions.call("Helm:getMolfiles",{col:i});T(n.length,i.length);const r=n.toList().map(t=>fi.getInstance(t));E(r.map(t=>t.atomCount),e.getCol("atoms").toList()),E(r.map(t=>t.bondCount),e.getCol("bonds").toList()),Ti.logger.debug("Helm/getMolfiles/linear1, grid awaiting 2"),await X(s.grid,5e3),Ti.logger.debug("Helm/getMolfiles/linear1, grid awaited 2")})});class mi extends Error{constructor(t,e){super(t,e)}}async function yi(t,e){const i=K.div([],{style:{width:"0",height:"0"}});document.documentElement.appendChild(i);try{if(t.length>1e3)throw new mi("Too long sequence to calculate molecular properties.");const s=(e.isHelm()?t:e.getConverter(ut.HELM)(t)).replaceAll(H,"{").replaceAll(B,".").replaceAll(G,"}").replace("{*}","{}"),n=(await j()).createHelmWebEditor(i).editor;n.setHelm(s);const r=n.getFormula(!0),o=Math.round(100*n.getMolWeight())/100,l=Math.round(100*n.getExtinctionCoefficient())/100;return{formula:r.replace(/<sub>/g,"").replace(/<\/sub>/g,""),"molecular weight":o,"extinction coefficient":l}}finally{ht()(i).empty(),i.remove()}}const bi={Helm:{seq:"PEPTIDE1{I.H.A.C.T.[Thr_PO3H2].[Aca].[D-Tyr_Et]}|PEPTIDE2{E.A.[meG]}$PEPTIDE1,PEPTIDE2,4:R3-1:R1$$$V2.0",units:ut.HELM,res:{formula:"C58H94N13O21SP","molecular weight":1372.49,"extinction coefficient":1.55}},separator:{seq:"I/H/A/C/T/Thr_PO3H2/Aca/D-Tyr_Et",units:ut.SEPARATOR,separator:"/",alphabet:pt.UN,res:{formula:"C47H77N10O15SP","molecular weight":1085.22,"extinction coefficient":1.55}},separator2:{seq:"meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Aze/dV/E/N////Phe_4Me",units:ut.SEPARATOR,separator:"/",alphabet:pt.UN,res:{formula:"C91H146N19O25P","molecular weight":1937.25,"extinction coefficient":1.49}},"separator-gaps":{seq:"I/H/A//T/Thr_PO3H2/Aca/D-Tyr_Et",units:ut.SEPARATOR,separator:"/",alphabet:pt.UN,res:{formula:"C44H72N9O14P","molecular weight":982.08,"extinction coefficient":1.49}},"fasta-PT":{seq:"IHACTTAY",units:ut.FASTA,alphabet:pt.PT,res:{formula:"C38H58N10O12S","molecular weight":879,"extinction coefficient":1.55}},"fasta-RNA":{seq:"ACGUAUUCC",units:ut.FASTA,alphabet:pt.RNA,res:{formula:"C84H107N30O65P9","molecular weight":2855.69,"extinction coefficient":86.96}},"fasta-DNA":{seq:"ACGTATTCC",units:ut.FASTA,alphabet:pt.DNA,res:{formula:"C87H113N30O56P9","molecular weight":2753.78,"extinction coefficient":86.96}}};function _i(t,e,i){const s=i.parse(t);T(s.atoms.length,e.atomCount),T(s.bonds.length,e.bondCount),T(s.atoms.every(t=>!t.elem.startsWith("[")&&!t.elem.endsWith("]")),!0,"Atoms should not contain square braces.")}var Ci;P("properties-widget",()=>{let e,i,s=null;k(async()=>{await Q(),e=await gi(),i=await Z(),s=lt(),await i.loadMonomerLibForTests()}),S(async()=>{await at(s),await i.loadMonomerLib(!0)});for(const[t,e]of Object.entries(bi))w(t,async()=>{await n(e.seq,e.units,e.separator,e.alphabet,e.res)});async function n(i,s,n,r,o){const l=t.Column.fromStrings("seq",[i]);l.semType=t.SEMTYPE.MACROMOLECULE,l.meta.units=s,n&&l.setTag(ft.separator,n),r&&l.setTag(ft.alphabet,r);const a=e.getSeqHandler(l);A(await yi(i,a),o)}w("too-long",async()=>{const i=function(e=1e4){const i="meI/hHis/Aca/N//dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe".repeat(Math.ceil(e/10)).slice(0,-1),s=t.Column.fromList(t.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(i));s.semType=t.SEMTYPE.MACROMOLECULE,s.meta.units=ut.SEPARATOR,s.setTag(ft.separator,"/"),s.setTag(ft.alphabet,pt.UN),s.setTag(ft.alphabetIsMultichar,"true");const n=[];return n.push(s),n.push(t.Column.fromList(t.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),n}(),s=t.DataFrame.fromColumns(i).getCol("MSA"),n=e.getSeqHandler(s);let r=!0;try{await yi(s.get(0),n)}catch(t){t instanceof mi&&(r=!0)}T(r,!0)})}),P("parseHelm",()=>{const t={PT:{src:"PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0",tgt:{atomCount:6,bondCount:5,helm:"PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0"}},"PT-cyclic":{src:"PEPTIDE1{[meI].C.[Aca].[Cys_SEt].T.C.[Thr_PO3H2].[Aca]}$PEPTIDE1,PEPTIDE1,8:R2-1:R1$$$V2.0",tgt:{atomCount:8,bondCount:8,helm:"PEPTIDE1{[meI].C.[Aca].[Cys_SEt].T.C.[Thr_PO3H2].[Aca]}$PEPTIDE1,PEPTIDE1,8:R2-1:R1$$$V2.0"}},RNA:{src:"RNA1{[dhp]([m1A])p.r(T)p.r(T)p.r(G)p}$$$$V2.0",tgt:{atomCount:12,bondCount:11,helm:"RNA1{[dhp]([m1A])p.r(T)p.r(T)p.r(G)p}$$$$V2.0"}},"PT-with-gap":{src:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$$$$V2.0",tgt:{atomCount:8,bondCount:7,helm:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$$$$V2.0"}},"PT-with-gap-at-connection":{src:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0",tgt:{atomCount:8,bondCount:8,helm:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0"}}};let e,i,s;k(async()=>{await Q(),e=await j(),i=await Z(),s=await lt(),await i.loadMonomerLibForTests()}),S(async()=>{await at(s),await i.loadMonomerLib(!0)});for(const[i,{src:s,tgt:n}]of Object.entries(t))w(`HelmHelper-${i}`,async()=>{_i(s,n,e)})}),P("helm-web-editor",async()=>{let t,e,i;k(async()=>{await Q(),t=await Z(),e=await lt(),await t.loadMonomerLibForTests(),i=await j()}),S(async()=>{await at(e),await t.loadMonomerLib(!0)}),w("helm-web-editor",async()=>{i.createHelmWebEditor()}),w("web-editor-app",async()=>{const t=K.div([],{style:{width:"700px",height:"432px"}});i.createWebEditorApp(t,"PEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$"),K.dialog().add(t).show().close()})}),P("HelmInput",()=>{let t,e,i;k(async()=>{t=await j(),e=await Z(),i=await lt(),await e.loadMonomerLibForTests()}),S(async()=>{await at(i),await e.loadMonomerLib(!0)}),w("inDialog",async()=>{const t=await K.input.helmAsync("Macromolecule");t.stringValue="PEPTIDE1{[meY].A.G.T}$$$$",K.dialog("Helm Input Test").add(t).show(),await R(500);const e=t.molValue;T(e.atoms.length,4),T(e.bonds.length,3)}),w("renders-with-nonzero-height (root in a dialog)",async()=>{const t=await K.input.helmAsync("Macromolecule");t.stringValue="PEPTIDE1{[meY].A.G.T}$$$$";const e=K.dialog("Helm Input Height Test").add(t).show();try{await R(500);const e=t.getInput();T(e.clientHeight>0,!0,`editor host height must be > 0 (was ${e.clientHeight})`);const i=e.querySelector("svg");T(null!=i,!0,"an SVG must be mounted in the editor host");const s=i.getBoundingClientRect().height;T(s>0,!0,`mounted SVG height must be > 0 (was ${s})`)}finally{e.close()}}),w("default size is 250x250",async()=>{const t=await K.input.helmAsync("Macromolecule");t.stringValue="PEPTIDE1{[meY].A.G.T}$$$$";const e=K.dialog("Helm Input Default Size").add(t).show();try{await R(500);const e=t.getInput();T(Math.abs(e.clientWidth-250)<=4,!0,`default width ~250 (was ${e.clientWidth})`),T(Math.abs(e.clientHeight-250)<=4,!0,`default height ~250 (was ${e.clientHeight})`)}finally{e.close()}}),w("editorOptions.width/height override the default size",async()=>{const t=await K.input.helmAsync("Macromolecule",{editable:!0,editorOptions:{width:320,height:180}});t.stringValue="PEPTIDE1{[meY].A.G.T}$$$$";const e=K.dialog("Helm Input Custom Size").add(t).show();try{await R(500);const e=t.getInput();T(Math.abs(e.clientWidth-320)<=4,!0,`width ~320 from editorOptions (was ${e.clientWidth})`),T(Math.abs(e.clientHeight-180)<=4,!0,`height ~180 from editorOptions (was ${e.clientHeight})`)}finally{e.close()}}),w("editor canvas sizes from getInput() box (consumer sets height on the host)",async()=>{const t=await K.input.helmAsync("Macromolecule");t.stringValue="PEPTIDE1{[meY].A.G.T}$$$$";const e=K.dialog("Helm getInput() Size Test").add(t).show();try{await R(300);const e=t.getInput();e.style.setProperty("width","360px","important"),e.style.setProperty("height","260px","important"),await R(500),T(e.clientWidth,360,`host width (was ${e.clientWidth})`),T(e.clientHeight,260,`host height (was ${e.clientHeight})`);const i=e.querySelector("svg");T(null!=i,!0,"an SVG must be mounted");const s=i.getBoundingClientRect();T(s.height>=e.clientHeight-8,!0,`SVG height should track the host's ${e.clientHeight} (was ${s.height})`),T(s.width>=e.clientWidth-8,!0,`SVG width should track the host's ${e.clientWidth} (was ${s.width})`)}finally{e.close()}}),w("tooltip",async()=>{await async function(){const t=await K.input.helmAsync("Macromolecule");t.stringValue="PEPTIDE1{[meY].A.G.T}$$$$";const e=tt.shell.v?tt.shell.v.root.getBoundingClientRect():null,i=K.dialog("Helm Input Test").add(t).show({...e?{x:e.right+20,y:e.top+20}:{}});try{const e=ht()(i.root).find("div.d4-dialog-contents > div.ui-input-helm > div.ui-input-editor").get(0);T(t.getInput(),e);const s={i:0,elem:"meY"},n=t.molValue.atoms[s.i],r=t.getInput(),o=r.getBoundingClientRect(),l=new MouseEvent("mousemove",{cancelable:!0,bubbles:!0,view:window,button:0,clientX:o.left+n.p.x,clientY:o.top+n.p.y});await v(K.tooltip.onTooltipShown,()=>{},()=>{r.dispatchEvent(l)},100,"timeout await ui.tooltip.onTooltipShown");const a=ht()(document).find("body > div.d4-tooltip").get(0),c=ht()(a).find("div > div.d4-flex-row.ui-div > div:nth-child(1)").get(0);T("none"!=a.style.display,!0),T(c?.innerText,s.elem)}finally{await R(50),K.tooltip.hide()}}()},{timeout:3e5})}),P("HelmHelper: removeGaps",()=>{let t,e,i;k(async()=>{t=await j(),e=await Z(),i=await lt(),await e.loadMonomerLibForTests()}),S(async()=>{await at(i),await e.loadMonomerLib(!0)});const s={"single-linear-start":{src:{helm:"PEPTIDE1{*.[meY].A.G.T}$$$$V2.0"},tgt:{helm:"PEPTIDE1{[meY].A.G.T}$$$$V2.0",map:[[1,0],[2,1],[3,2],[4,3]]}},"single-linear-end":{src:{helm:"PEPTIDE1{[meY].A.G.T.*}$$$$V2.0"},tgt:{helm:"PEPTIDE1{[meY].A.G.T}$$$$V2.0",map:[[0,0],[1,1],[2,2],[3,3]]}},"single-linear-middle":{src:{helm:"PEPTIDE1{[meY].A.*.G.T}$$$$V2.0"},tgt:{helm:"PEPTIDE1{[meY].A.G.T}$$$$V2.0",map:[[0,0],[1,1],[3,2],[4,3]]}},"single-cycle-start":{src:{helm:"PEPTIDE1{*.[meY].C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,3:R3-7:R3$$$V2.0"},tgt:{helm:"PEPTIDE1{[meY].C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0",map:[[1,0],[2,1],[3,2],[4,3],[5,4],[6,5],[7,6]]}},"single-cycle-end":{src:{helm:"PEPTIDE1{[meY].C.R.N.P.C.T.*}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0"},tgt:{helm:"PEPTIDE1{[meY].C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0",map:[[0,0],[1,1],[2,2],[3,3],[4,4],[5,5],[6,6]]}},"single-cycle-middle":{src:{helm:"PEPTIDE1{[meY].C.R.N.*.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0"},tgt:{helm:"PEPTIDE1{[meY].C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0",map:[[0,0],[1,1],[2,2],[3,3],[5,4],[6,5],[7,6]]}},"single-cycle-gap-at-connection":{src:{helm:"PEPTIDE1{[meY].*.C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0"},tgt:{helm:null,map:[],errType:"HelmNotSupportedError"}}};for(const[e,i]of Object.entries(s))w(`${e}`,async()=>{let e=null;try{const e=t.removeGaps(i.src.helm);T(e.resHelm,i.tgt.helm),E(Array.from(e.monomerMap.entries()),i.tgt.map)}catch(t){e=t}i.tgt.errType&&T(e?.type,i.tgt.errType,"HelmNotSupportedError thrown expected")})});class vi{constructor(t,e=!0,i){return this.substructure=t,this.readOnly=e,this.logger=i,new Proxy(this,{set:(t,e,i)=>{if(this.logger?.debug(`BioFilterProps.set ${e.toString()}( '${i}' )`),this.readOnly)throw new Error("Properties are immutable.");return t[e]=i,!0}})}}P("bio-substructure-filters",async()=>{let t,e,i;async function s(t,e){if(!e.columns.names().includes(t))throw new Error(`The column '${t}' not found. Available in data frame are ${JSON.stringify(e.columns.names())}`);const i=await tt.functions.call("Bio:bioSubstructureFilterTest");return i.attach(e),i.applyState({columnName:t}),i.column=e.col(t),i.columnName=t,i}k(async()=>{t=await gi(),e=await Z(),i=await lt(),await e.loadMonomerLibForTests()}),S(async()=>{await at(i),await e.loadMonomerLib(!0)}),w("helm-dialog",async()=>{const t="Bio tests: substructureFilters/helm-dialog",e=await J("tests/filter_HELM.csv"),i=tt.shell.addTableView(e);await tt.data.detectSemanticTypes(e),await e.meta.detectSemanticTypes(),Ti.logger.debug(`${t}, filter attaching.`);const s=await tt.functions.call("Bio:bioSubstructureFilterTest");s.attach(e);const n=K.dialog("Test filters").add(s.root).show();await s.awaitRendered();try{const n=s.bioFilter;T(null!==s.bioFilter,!0,"bioFilter is not created"),Ti.logger.debug(`${t}, filter 1 change awaiting...`),await v(e.onRowsFiltered,()=>{},()=>{n.props=new vi("PEPTIDE1{A.C}$$$$V2.0",void 0,Ti.logger)},2e4),Ti.logger.debug(`${t}, filter 1 changed.`),T(s.dataFrame.filter.trueCount,1),T(s.dataFrame.filter.toBinaryString(),"0001"),Ti.logger.debug(`${t}, filter 2 change awaiting...`),await v(e.onRowsFiltered,()=>{},()=>{n.props=new vi("PEPTIDE1{C}$$$$V2.0",void 0,Ti.logger)},2e4),setTimeout(()=>i.grid.invalidate(),500),await X(i.grid),await R(1e3),Ti.logger.debug(`${t}, filter 2 changed.`),T(s.dataFrame.filter.trueCount,2),T(s.dataFrame.filter.toBinaryString(),"1001")}finally{n.close()}await s.awaitRendered(),await R(3e3)},{}),w("helm-view",async()=>{const t=await J("tests/filter_HELM.csv");t.getCol("HELM string"),await tt.data.detectSemanticTypes(t);const e=tt.shell.addTableView(t);e.getFiltersGroup(),await X(e.grid)}),w("sync-helm",async()=>{const t=await Ti.files.readCsv("tests/filter_HELM.csv");await tt.data.detectSemanticTypes(t);const e=tt.shell.addTableView(t),i="PEPTIDE1{A.C}$$$$V2.0",n=await s("HELM string",t),r=await s("HELM string",t),o=K.dialog("Test filters").add(n.root).add(r.root).show();await Promise.all([n.awaitRendered(),r.awaitRendered()]);try{T(!!n.bioFilter,!0),T(!!r.bioFilter,!0),T(n.bioFilter.type,"HelmBioFilter"),T(r.bioFilter.type,"HelmBioFilter");const s=n.bioFilter,o=r.bioFilter;await v(t.onRowsFiltered,()=>{},()=>{s.props=new vi(i,void 0,Ti.logger)},6e4,"await onRowsFiltered"),await X(e.grid),Ti.logger.debug("Bio tests: substructureFilters/sync-helm, before changed event"),await R(2*n.debounceTime),Ti.logger.debug("Bio tests: substructureFilters/sync-helm, after changed event"),T(t.filter.trueCount,1),await n.awaitRendered(),T(o.props.substructure,i)}finally{n.detach(),r.detach(),o.close()}await Promise.all([n.awaitRendered(),r.awaitRendered()]),await X(e.grid),await R(3e3)})}),function(t){t.UMAP="UMAP",t.T_SNE="t-SNE"}(Ci||(Ci={}));new Uint32Array(65536);var wi;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(wi||(wi={})),wi.HAMMING,wi.LEVENSHTEIN,wi.NEEDLEMANN_WUNSCH,wi.MONOMER_CHEMICAL_DISTANCE;P("activityCliffs",async()=>{let e,i,s;const n=t.Func.find({name:"macromoleculePreprocessingFunction",package:"Bio"})[0];k(async()=>{e=await j(),i=await Z(),s=await lt(),await i.loadMonomerLibForTests()}),S(async()=>{await at(s),await i.loadMonomerLib(!0)}),w("Helm",async()=>{const e=await Ti.files.readCsv("samples/HELM_50.csv"),i=tt.shell.addTableView(e);await async function(e,i,s,n,r,o,l,a,c){await tt.data.detectSemanticTypes(i),await tt.functions.call("Bio:activityCliffs",{table:i,molecules:i.getCol("HELM"),activities:i.getCol("Activity"),similarity:65,methodName:s,similarityMetric:a,preprocessingFunction:c,options:{bypassLargeDataWarning:!0},demo:!1});const h=Array.from(e.viewers).find(e=>e.type===t.VIEWER.SCATTER_PLOT);T(null!=h,!0);await F(()=>(()=>{const t=h.root.getElementsByClassName("scatter_plot_link");return t.length>0&&"311 cliffs"===t[0].innerText.toLowerCase()})(),"activity cliffs failed")}(i,e,Ci.UMAP,0,0,0,0,wi.HAMMING,n)})}),P("toAtomicLevel-ui",()=>{let e,i,s,n;k(async()=>{n=await async function(){const e=t.Func.find({package:"Chem",name:"getRdKitModule"});if(0===e.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await e[0].prepare().call()).getOutputParamValue()}(),e=await Z(),i=await lt(),await e.loadMonomerLibForTests(),s=e.getMonomerLib()}),S(async()=>{await at(i),await e.loadMonomerLib(!0)});const r={fasta:{src:{seq:"MDYKETLLMPK",units:ut.FASTA},tgt:{atomCount:94,bondCount:95}},"fasta-with-gap":{src:{seq:"MD-YKETLLMPK",units:ut.FASTA},tgt:{atomCount:94,bondCount:95}},helm:{src:{seq:"PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2}$$$$",units:ut.HELM},tgt:{atomCount:68,bondCount:68}},"helm-with-gap":{src:{seq:"PEPTIDE1{meI.hHis.*.Aca.N.T.dK.Thr_PO3H2}$$$$",units:ut.HELM},tgt:{atomCount:68,bondCount:68}}},o=async e=>{const i=e.src.seq,s=t.DataFrame.fromColumns([t.Column.fromList(t.COLUMN_TYPE.STRING,"seq",[i])]);return await tt.data.detectSemanticTypes(s),{df:s,seqCol:s.getCol("seq")}};for(const[t,e]of Object.entries(r))w(`${t}-nonlinear`,async()=>{const t=await o(e);await l(t.df,t.seqCol,0,e.tgt)});async function l(e,i,s,r){await tt.functions.call("Bio:toAtomicLevel",{table:e,seqCol:i,nonlinear:!0,highlight:!1});const o=e.col("molfile(seq)");T(o?.semType,t.SEMTYPE.MOLECULE);const l=o?.get(0),a=n.get_mol(l);T(null!=a,!0,"No molecule generated");try{const t=a.get_num_atoms(),e=a.get_num_bonds();T(t,r.atomCount),T(e,r.bondCount)}finally{a.delete()}}});const Ti=new t.Package;async function xi(e,i,s){const u=await function(t){var e,i,s;return n(this,void 0,void 0,function*(){const u=(null==t?void 0:t.nodeOptions)?t.nodeOptions.package:grok.functions.getCurrentCall().func.package;if(!u)throw new Error("Can't run tests outside of the package");const p=null===(e=u.packageOwner)||void 0===e?void 0:e.match(/<([^>]*)>/),f=p?p[1]:"";null!=u&&(yield M(u));const g=[];console.log("Running tests..."),console.log(t),null!=t||(t={}),null!==(i=(s=t).testContext)&&void 0!==i||(s.testContext=new _),grok.shell.clearLastError();const m=function(){const t=[];return console.log=(...e)=>{t.push(...e),l(...e)},console.info=(...e)=>{t.push(...e),a(...e)},console.warn=(...e)=>{t.push(...e),c(...e)},console.error=(...e)=>{t.push(...e),h(...e)},t}();yield function(t,e){var i,s,r,o,d,p;return n(this,void 0,void 0,function*(){try{let a=null!=(null==e?void 0:e.skipToCategory),c=!1;for(const[h,m]of Object.entries(t)){if(null===(i=e.exclude)||void 0===i?void 0:i.some(t=>h.startsWith(t)))continue;if(null!=(null==e?void 0:e.category)&&!h.toLowerCase().startsWith(null==e?void 0:e.category.toLowerCase().trim()))continue;if(a)if(c)a=!1;else{if(null==(null==e?void 0:e.skipToCategory)||h.toLowerCase().trim()!==(null==e?void 0:e.skipToCategory.toLowerCase().trim()))continue;c=!0}const t=null===(s=m.tests)||void 0===s?void 0:s.every(t=>{var i;return(null===(i=t.options)||void 0===i?void 0:i.skipReason)||null!=(null==e?void 0:e.test)&&e.test.toLowerCase()!==t.name.toLowerCase()});if(!t){const t=(null!==(r=m.tests)&&void 0!==r?r:[]).filter(t=>{var i;return(null===(i=t.options)||void 0===i?void 0:i.skipReason)||null!=(null==e?void 0:e.test)&&e.test.toLowerCase()!==t.name.toLowerCase()}).length;l(`Package testing: Started {{${h}}}${t>0?` skipped {{${t}}}`:""}`),m.beforeStatus=yield y(m.before,h)}let _,C=null!==(o=m.tests)&&void 0!==o?o:[];e.stressTest&&(C=C.filter(t=>{var e;return null===(e=t.options)||void 0===e?void 0:e.stressTest}),C=O(C)),(null!==(p=null===(d=e.tags)||void 0===d?void 0:d.length)&&void 0!==p?p:0)>0&&(C=C.filter(t=>{var i,s;return null===(s=null===(i=t.options)||void 0===i?void 0:i.tags)||void 0===s?void 0:s.some(t=>{var i;return(null!==(i=null==e?void 0:e.tags)&&void 0!==i?i:[]).includes(t)})})),m.beforeStatus?(_=Array.from(C.map(t=>({date:(new Date).toISOString(),category:h,name:t.name,success:!1,result:"before() failed",ms:0,skipped:!1,logs:"",owner:f,package:u.name,widgetsDifference:0,flaking:DG.Test.isReproducing}))),_.forEach(t=>n(this,void 0,void 0,function*(){return yield grok.shell.reportTest("package",t)}))):_=yield b(m,e,a);const v=_.filter(t=>"skipped"!=t.result);if(t||(m.afterStatus=yield y(m.after,h)),m.afterStatus&&(l(`Package testing: Category after() {{${h}}} failed`),l(`Package testing: Result for {{${h}}} after: ${m.afterStatus}`),v.push({date:(new Date).toISOString(),category:h,name:"after",success:!1,result:m.afterStatus,ms:0,skipped:!1,logs:"",owner:f,package:u.name,widgetsDifference:0,flaking:DG.Test.isReproducing})),m.beforeStatus&&(l(`Package testing: Category before() {{${h}}} failed`),l(`Package testing: Result for {{${h}}} before: ${m.beforeStatus}`),v.push({date:(new Date).toISOString(),category:h,name:"before",success:!1,result:m.beforeStatus,ms:0,skipped:!1,logs:"",owner:f,package:u.name,widgetsDifference:0,flaking:DG.Test.isReproducing})),g.push(...v),e.returnOnFail&&v.some(t=>!t.success&&!t.skipped&&t.name!==e.skipToTest))break}}finally{console.log=l,console.info=a,console.warn=c,console.error=h}if(e.testContext.catchUnhandled&&!DG.Test.isInBenchmark){yield R(1e3);const t=yield grok.shell.lastError;if(null!=t){const e={logs:"",date:(new Date).toISOString(),category:"Unhandled exceptions",name:"Exception",result:null!=t?t:"",success:!t,ms:0,skipped:!1,owner:null!=f?f:"",package:u.name,widgetsDifference:0};l(`Package testing: Unhandled Exception: ${t}`),g.push(Object.assign(Object.assign({},e),{flaking:DG.Test.isReproducing&&!t})),e.package=u.name,yield grok.shell.reportTest("package",e)}}})}(d,t);for(let t of g)t.result=t.result.toString().replace(/"/g,"'"),null!=t.logs&&(t.logs=t.logs.toString().replace(/"/g,"'"));return g;function y(t,e){return n(this,void 0,void 0,function*(){let i;try{void 0!==t&&(yield D(()=>n(this,void 0,void 0,function*(){yield t()}),1e5,`before ${e}: timeout error`))}catch(t){i=yield N(t)}return i})}function b(t,e,i){var s,l,a,c,h,d,p,g,y,b,_,v,w,T,x,A,E,P,k;return n(this,void 0,void 0,function*(){let n=null!==(s=t.tests)&&void 0!==s?s:[];const S=[],$=C();if(t.clear){let s=i&&null!=e.skipToTest;for(let i=0;i<n.length;i++){n[i].options&&void 0===(null===(l=n[i].options)||void 0===l?void 0:l.benchmark)&&(n[i].options||(n[i].options={}),n[i].options.benchmark=null!==(a=t.benchmarks)&&void 0!==a&&a);let w=n[i];if(e.test&&e.test.toLowerCase()!==w.name.toLowerCase())continue;if(s){if(null==(null==e?void 0:e.skipToTest)||w.name.toLowerCase().trim()!==(null==e?void 0:e.skipToTest.toLowerCase().trim()))continue;s=!1}(null==w?void 0:w.options)&&(w.options.owner=null!==(p=null!==(d=null!==(h=null===(c=n[i].options)||void 0===c?void 0:c.owner)&&void 0!==h?h:null==t?void 0:t.owner)&&void 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