@datagrok-libraries/bio 5.62.0 → 5.63.0

package/src/utils/macromolecule/numbering-schemes.js

@@ -0,0 +1,149 @@
+/** Static antibody numbering scheme region definitions.
+ *
+ * Contains FR/CDR boundaries for IMGT, Kabat, Chothia, and AHo schemes.
+ * These are the canonical position ranges used after a numbering tool
+ * (e.g. ANARCI) has assigned scheme-specific position names.
+ */
+export var NumberingScheme;
+(function (NumberingScheme) {
+    NumberingScheme["IMGT"] = "IMGT";
+    NumberingScheme["Kabat"] = "Kabat";
+    NumberingScheme["Chothia"] = "Chothia";
+    NumberingScheme["AHo"] = "AHo";
+})(NumberingScheme || (NumberingScheme = {}));
+export var ChainType;
+(function (ChainType) {
+    ChainType["Heavy"] = "Heavy";
+    ChainType["Light_Kappa"] = "Light_Kappa";
+    ChainType["Light_Lambda"] = "Light_Lambda";
+})(ChainType || (ChainType = {}));
+/** IMGT region boundaries — the reference numbering scheme.
+ * @see https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html
+ */
+export const IMGT_REGIONS = {
+    [ChainType.Heavy]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '26', chainType: ChainType.Heavy },
+        { name: 'CDR1', type: 'CDR', startPosition: '27', endPosition: '38', chainType: ChainType.Heavy },
+        { name: 'FR2', type: 'FR', startPosition: '39', endPosition: '55', chainType: ChainType.Heavy },
+        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '65', chainType: ChainType.Heavy },
+        { name: 'FR3', type: 'FR', startPosition: '66', endPosition: '104', chainType: ChainType.Heavy },
+        { name: 'CDR3', type: 'CDR', startPosition: '105', endPosition: '117', chainType: ChainType.Heavy },
+        { name: 'FR4', type: 'FR', startPosition: '118', endPosition: '128', chainType: ChainType.Heavy },
+    ],
+    [ChainType.Light_Kappa]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '26', chainType: ChainType.Light_Kappa },
+        { name: 'CDR1', type: 'CDR', startPosition: '27', endPosition: '38', chainType: ChainType.Light_Kappa },
+        { name: 'FR2', type: 'FR', startPosition: '39', endPosition: '55', chainType: ChainType.Light_Kappa },
+        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '65', chainType: ChainType.Light_Kappa },
+        { name: 'FR3', type: 'FR', startPosition: '66', endPosition: '104', chainType: ChainType.Light_Kappa },
+        { name: 'CDR3', type: 'CDR', startPosition: '105', endPosition: '117', chainType: ChainType.Light_Kappa },
+        { name: 'FR4', type: 'FR', startPosition: '118', endPosition: '127', chainType: ChainType.Light_Kappa },
+    ],
+    [ChainType.Light_Lambda]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '26', chainType: ChainType.Light_Lambda },
+        { name: 'CDR1', type: 'CDR', startPosition: '27', endPosition: '38', chainType: ChainType.Light_Lambda },
+        { name: 'FR2', type: 'FR', startPosition: '39', endPosition: '55', chainType: ChainType.Light_Lambda },
+        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '65', chainType: ChainType.Light_Lambda },
+        { name: 'FR3', type: 'FR', startPosition: '66', endPosition: '104', chainType: ChainType.Light_Lambda },
+        { name: 'CDR3', type: 'CDR', startPosition: '105', endPosition: '117', chainType: ChainType.Light_Lambda },
+        { name: 'FR4', type: 'FR', startPosition: '118', endPosition: '127', chainType: ChainType.Light_Lambda },
+    ],
+};
+/** Kabat region boundaries (differ mainly in CDR definitions). */
+export const KABAT_REGIONS = {
+    [ChainType.Heavy]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '30', chainType: ChainType.Heavy },
+        { name: 'CDR1', type: 'CDR', startPosition: '31', endPosition: '35', chainType: ChainType.Heavy },
+        { name: 'FR2', type: 'FR', startPosition: '36', endPosition: '49', chainType: ChainType.Heavy },
+        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '65', chainType: ChainType.Heavy },
+        { name: 'FR3', type: 'FR', startPosition: '66', endPosition: '94', chainType: ChainType.Heavy },
+        { name: 'CDR3', type: 'CDR', startPosition: '95', endPosition: '102', chainType: ChainType.Heavy },
+        { name: 'FR4', type: 'FR', startPosition: '103', endPosition: '113', chainType: ChainType.Heavy },
+    ],
+    [ChainType.Light_Kappa]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '23', chainType: ChainType.Light_Kappa },
+        { name: 'CDR1', type: 'CDR', startPosition: '24', endPosition: '34', chainType: ChainType.Light_Kappa },
+        { name: 'FR2', type: 'FR', startPosition: '35', endPosition: '49', chainType: ChainType.Light_Kappa },
+        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '56', chainType: ChainType.Light_Kappa },
+        { name: 'FR3', type: 'FR', startPosition: '57', endPosition: '88', chainType: ChainType.Light_Kappa },
+        { name: 'CDR3', type: 'CDR', startPosition: '89', endPosition: '97', chainType: ChainType.Light_Kappa },
+        { name: 'FR4', type: 'FR', startPosition: '98', endPosition: '107', chainType: ChainType.Light_Kappa },
+    ],
+    [ChainType.Light_Lambda]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '23', chainType: ChainType.Light_Lambda },
+        { name: 'CDR1', type: 'CDR', startPosition: '24', endPosition: '34', chainType: ChainType.Light_Lambda },
+        { name: 'FR2', type: 'FR', startPosition: '35', endPosition: '49', chainType: ChainType.Light_Lambda },
+        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '56', chainType: ChainType.Light_Lambda },
+        { name: 'FR3', type: 'FR', startPosition: '57', endPosition: '88', chainType: ChainType.Light_Lambda },
+        { name: 'CDR3', type: 'CDR', startPosition: '89', endPosition: '97', chainType: ChainType.Light_Lambda },
+        { name: 'FR4', type: 'FR', startPosition: '98', endPosition: '107', chainType: ChainType.Light_Lambda },
+    ],
+};
+/** Chothia region boundaries. */
+export const CHOTHIA_REGIONS = {
+    [ChainType.Heavy]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '25', chainType: ChainType.Heavy },
+        { name: 'CDR1', type: 'CDR', startPosition: '26', endPosition: '32', chainType: ChainType.Heavy },
+        { name: 'FR2', type: 'FR', startPosition: '33', endPosition: '51', chainType: ChainType.Heavy },
+        { name: 'CDR2', type: 'CDR', startPosition: '52', endPosition: '56', chainType: ChainType.Heavy },
+        { name: 'FR3', type: 'FR', startPosition: '57', endPosition: '94', chainType: ChainType.Heavy },
+        { name: 'CDR3', type: 'CDR', startPosition: '95', endPosition: '102', chainType: ChainType.Heavy },
+        { name: 'FR4', type: 'FR', startPosition: '103', endPosition: '113', chainType: ChainType.Heavy },
+    ],
+    [ChainType.Light_Kappa]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '25', chainType: ChainType.Light_Kappa },
+        { name: 'CDR1', type: 'CDR', startPosition: '26', endPosition: '32', chainType: ChainType.Light_Kappa },
+        { name: 'FR2', type: 'FR', startPosition: '33', endPosition: '49', chainType: ChainType.Light_Kappa },
+        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '52', chainType: ChainType.Light_Kappa },
+        { name: 'FR3', type: 'FR', startPosition: '53', endPosition: '90', chainType: ChainType.Light_Kappa },
+        { name: 'CDR3', type: 'CDR', startPosition: '91', endPosition: '96', chainType: ChainType.Light_Kappa },
+        { name: 'FR4', type: 'FR', startPosition: '97', endPosition: '107', chainType: ChainType.Light_Kappa },
+    ],
+    [ChainType.Light_Lambda]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '25', chainType: ChainType.Light_Lambda },
+        { name: 'CDR1', type: 'CDR', startPosition: '26', endPosition: '32', chainType: ChainType.Light_Lambda },
+        { name: 'FR2', type: 'FR', startPosition: '33', endPosition: '49', chainType: ChainType.Light_Lambda },
+        { name: 'CDR2', type: 'CDR', startPosition: '50', endPosition: '52', chainType: ChainType.Light_Lambda },
+        { name: 'FR3', type: 'FR', startPosition: '53', endPosition: '90', chainType: ChainType.Light_Lambda },
+        { name: 'CDR3', type: 'CDR', startPosition: '91', endPosition: '96', chainType: ChainType.Light_Lambda },
+        { name: 'FR4', type: 'FR', startPosition: '97', endPosition: '107', chainType: ChainType.Light_Lambda },
+    ],
+};
+/** AHo region boundaries. */
+export const AHO_REGIONS = {
+    [ChainType.Heavy]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '24', chainType: ChainType.Heavy },
+        { name: 'CDR1', type: 'CDR', startPosition: '25', endPosition: '40', chainType: ChainType.Heavy },
+        { name: 'FR2', type: 'FR', startPosition: '41', endPosition: '55', chainType: ChainType.Heavy },
+        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '78', chainType: ChainType.Heavy },
+        { name: 'FR3', type: 'FR', startPosition: '79', endPosition: '108', chainType: ChainType.Heavy },
+        { name: 'CDR3', type: 'CDR', startPosition: '109', endPosition: '138', chainType: ChainType.Heavy },
+        { name: 'FR4', type: 'FR', startPosition: '139', endPosition: '149', chainType: ChainType.Heavy },
+    ],
+    [ChainType.Light_Kappa]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '24', chainType: ChainType.Light_Kappa },
+        { name: 'CDR1', type: 'CDR', startPosition: '25', endPosition: '40', chainType: ChainType.Light_Kappa },
+        { name: 'FR2', type: 'FR', startPosition: '41', endPosition: '55', chainType: ChainType.Light_Kappa },
+        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '78', chainType: ChainType.Light_Kappa },
+        { name: 'FR3', type: 'FR', startPosition: '79', endPosition: '108', chainType: ChainType.Light_Kappa },
+        { name: 'CDR3', type: 'CDR', startPosition: '109', endPosition: '138', chainType: ChainType.Light_Kappa },
+        { name: 'FR4', type: 'FR', startPosition: '139', endPosition: '149', chainType: ChainType.Light_Kappa },
+    ],
+    [ChainType.Light_Lambda]: [
+        { name: 'FR1', type: 'FR', startPosition: '1', endPosition: '24', chainType: ChainType.Light_Lambda },
+        { name: 'CDR1', type: 'CDR', startPosition: '25', endPosition: '40', chainType: ChainType.Light_Lambda },
+        { name: 'FR2', type: 'FR', startPosition: '41', endPosition: '55', chainType: ChainType.Light_Lambda },
+        { name: 'CDR2', type: 'CDR', startPosition: '56', endPosition: '78', chainType: ChainType.Light_Lambda },
+        { name: 'FR3', type: 'FR', startPosition: '79', endPosition: '108', chainType: ChainType.Light_Lambda },
+        { name: 'CDR3', type: 'CDR', startPosition: '109', endPosition: '138', chainType: ChainType.Light_Lambda },
+        { name: 'FR4', type: 'FR', startPosition: '139', endPosition: '149', chainType: ChainType.Light_Lambda },
+    ],
+};
+/** Lookup table: scheme → chain type → region defs */
+export const SCHEME_REGIONS = {
+    [NumberingScheme.IMGT]: IMGT_REGIONS,
+    [NumberingScheme.Kabat]: KABAT_REGIONS,
+    [NumberingScheme.Chothia]: CHOTHIA_REGIONS,
+    [NumberingScheme.AHo]: AHO_REGIONS,
+};
+//# sourceMappingURL=numbering-schemes.js.map

package/src/utils/macromolecule/numbering-schemes.js.map

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package/src/utils/monomer-selection-dialog.d.ts

@@ -0,0 +1,47 @@
+import { PolymerType } from '../helm/types';
+import { IMonomerLib, IMonomerLibHelper } from '../types/monomer-library';
+export declare function parseMonomerSymbolList(src: string): string[];
+/** Embeddable widget for selecting monomers with autocomplete, tag-based display,
+ * and bulk-add from monomer libraries or collections.
+ * Can be embedded directly into any container (dialog, panel, etc.). */
+export declare class MonomerSelectionWidget {
+    private readonly selectedMonomers;
+    private readonly monomerLib;
+    private polymerType;
+    private helmType;
+    private allSymbols;
+    private readonly libHelper?;
+    private readonly tagsHost;
+    private readonly countLabel;
+    private readonly inputEl;
+    private currentMenu;
+    private menuItems;
+    private highlightedIndex;
+    /** The root element to embed in a container */
+    readonly root: HTMLDivElement;
+    constructor(monomerLib: IMonomerLib, polymerType: PolymerType, presetMonomers?: string[], libHelper?: IMonomerLibHelper);
+    /** Returns the currently selected monomer symbols */
+    getSelectedMonomers(): string[];
+    /** Sets new monomer selections, replacing existing ones */
+    setSelectedMonomers(symbols: string[]): void;
+    /** Updates the polymer type and refreshes the available symbols list */
+    setPolymerType(polymerType: PolymerType): void;
+    /** Focuses the search input */
+    focus(): void;
+    private updateCountLabel;
+    private renderTags;
+    private addMonomer;
+    private addMonomers;
+    private hideMenu;
+    private getSuggestions;
+    private showSuggestions;
+    private updateHighlight;
+    private setupInputListeners;
+    private createLibrarySection;
+    private createCollectionSection;
+}
+/** Shows a dialog for selecting monomers with autocomplete, tag-based display,
+ * and bulk-add from monomer libraries or collections.
+ * @returns monomer symbols array, or null if cancelled */
+export declare function showMonomerSelectionDialog(monomerLib: IMonomerLib, polymerType: PolymerType, presetMonomers?: string[], libHelper?: IMonomerLibHelper): Promise<string[] | null>;
+//# sourceMappingURL=monomer-selection-dialog.d.ts.map

package/src/utils/monomer-selection-dialog.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"monomer-selection-dialog.d.ts","sourceRoot":"","sources":["monomer-selection-dialog.ts"],"names":[],"mappings":"AAIA,OAAO,EAAW,WAAW,EAAC,MAAM,eAAe,CAAC;AACpD,OAAO,EAAC,WAAW,EAAE,iBAAiB,EAAU,MAAM,0BAA0B,CAAC;AAGjF,wBAAgB,sBAAsB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CAU5D;AAID;;wEAEwE;AACxE,qBAAa,sBAAsB;IACjC,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAW;IAC5C,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAc;IACzC,OAAO,CAAC,WAAW,CAAc;IACjC,OAAO,CAAC,QAAQ,CAAW;IAC3B,OAAO,CAAC,UAAU,CAAW;IAC7B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAoB;IAE/C,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAiB;IAC1C,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAiB;IAC5C,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAmB;IAC3C,OAAO,CAAC,WAAW,CAAwB;IAC3C,OAAO,CAAC,SAAS,CAAqB;IACtC,OAAO,CAAC,gBAAgB,CAAM;IAE9B,+CAA+C;IAC/C,SAAgB,IAAI,EAAE,cAAc,CAAC;gBAGnC,UAAU,EAAE,WAAW,EACvB,WAAW,EAAE,WAAW,EACxB,cAAc,CAAC,EAAE,MAAM,EAAE,EACzB,SAAS,CAAC,EAAE,iBAAiB;IA4C/B,qDAAqD;IACrD,mBAAmB,IAAI,MAAM,EAAE;IAI/B,2DAA2D;IAC3D,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI;IAM5C,wEAAwE;IACxE,cAAc,CAAC,WAAW,EAAE,WAAW,GAAG,IAAI;IAM9C,+BAA+B;IAC/B,KAAK,IAAI,IAAI;IAIb,OAAO,CAAC,gBAAgB;IAIxB,OAAO,CAAC,UAAU;IAkClB,OAAO,CAAC,UAAU;IAUlB,OAAO,CAAC,WAAW;IAYnB,OAAO,CAAC,QAAQ;IAShB,OAAO,CAAC,cAAc;IAuBtB,OAAO,CAAC,eAAe;IAuCvB,OAAO,CAAC,eAAe;IAYvB,OAAO,CAAC,mBAAmB;IAoE3B,OAAO,CAAC,oBAAoB;IAyC5B,OAAO,CAAC,uBAAuB;CAqChC;AAED;;0DAE0D;AAC1D,wBAAsB,0BAA0B,CAC9C,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,WAAW,EAAE,cAAc,CAAC,EAAE,MAAM,EAAE,EAC5E,SAAS,CAAC,EAAE,iBAAiB,GAC5B,OAAO,CAAC,MAAM,EAAE,GAAG,IAAI,CAAC,CAY1B"}

package/src/utils/monomer-selection-dialog.js

@@ -0,0 +1,354 @@
+/* eslint-disable max-len */
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import { polymerTypeToHelmType } from './macromolecule/utils';
+export function parseMonomerSymbolList(src) {
+    // L, L-hArg(Et,Et), "hArg(Et,Et)"
+    return src.split(/,(?![^(]*\))/)
+        .map((s) => {
+        s = s.trim();
+        if (s.slice(0, 1) === `"` && s.slice(-1) === `"`)
+            s = s.slice(1, -1);
+        if (s.slice(0, 1) === `'` && s.slice(-1) === `'`)
+            s = s.slice(1, -1);
+        return s.trim();
+    })
+        .filter((s) => !!s);
+}
+const MAX_SUGGESTIONS = 20;
+/** Embeddable widget for selecting monomers with autocomplete, tag-based display,
+ * and bulk-add from monomer libraries or collections.
+ * Can be embedded directly into any container (dialog, panel, etc.). */
+export class MonomerSelectionWidget {
+    constructor(monomerLib, polymerType, presetMonomers, libHelper) {
+        this.currentMenu = null;
+        this.menuItems = [];
+        this.highlightedIndex = -1;
+        this.monomerLib = monomerLib;
+        this.polymerType = polymerType;
+        this.helmType = polymerTypeToHelmType(polymerType);
+        this.allSymbols = monomerLib.getMonomerSymbolsByType(polymerType);
+        this.libHelper = libHelper;
+        this.selectedMonomers = presetMonomers ? [...presetMonomers] : [];
+        // --- Tags display (selected monomers) ---
+        this.tagsHost = ui.div([], { style: { display: 'flex', flexWrap: 'wrap', gap: '4px', marginTop: '4px', maxHeight: '150px', overflowY: 'auto' } });
+        this.countLabel = ui.divText('', { style: { fontSize: '11px', color: 'var(--grey-4)', marginTop: '4px' } });
+        // --- Autocomplete input ---
+        const input = ui.input.string('Search', { value: '' });
+        this.inputEl = input.input;
+        this.inputEl.setAttribute('autocomplete', 'off');
+        this.inputEl.placeholder = 'Type to search monomers...';
+        this.setupInputListeners();
+        // --- Bulk add sections ---
+        const librarySection = this.createLibrarySection();
+        const collectionSection = this.createCollectionSection();
+        // --- Clear all button ---
+        const clearBtn = ui.button('Clear all', () => {
+            this.selectedMonomers.length = 0;
+            this.renderTags();
+        });
+        clearBtn.style.fontSize = '11px';
+        clearBtn.style.marginTop = '4px';
+        this.renderTags();
+        this.root = ui.div([
+            input.root,
+            librarySection,
+            collectionSection,
+            ui.divH([this.countLabel, clearBtn], { style: { justifyContent: 'space-between', alignItems: 'center' } }),
+            this.tagsHost,
+        ], { style: { minWidth: '300px' } });
+    }
+    /** Returns the currently selected monomer symbols */
+    getSelectedMonomers() {
+        return [...this.selectedMonomers];
+    }
+    /** Sets new monomer selections, replacing existing ones */
+    setSelectedMonomers(symbols) {
+        this.selectedMonomers.length = 0;
+        this.selectedMonomers.push(...symbols);
+        this.renderTags();
+    }
+    /** Updates the polymer type and refreshes the available symbols list */
+    setPolymerType(polymerType) {
+        this.polymerType = polymerType;
+        this.helmType = polymerTypeToHelmType(polymerType);
+        this.allSymbols = this.monomerLib.getMonomerSymbolsByType(polymerType);
+    }
+    /** Focuses the search input */
+    focus() {
+        this.inputEl.focus();
+    }
+    updateCountLabel() {
+        this.countLabel.textContent = this.selectedMonomers.length > 0 ? `${this.selectedMonomers.length} monomer(s) selected` : '';
+    }
+    renderTags() {
+        this.tagsHost.innerHTML = '';
+        for (const symbol of this.selectedMonomers) {
+            const removeBtn = ui.iconFA('times', () => {
+                const idx = this.selectedMonomers.indexOf(symbol);
+                if (idx >= 0) {
+                    this.selectedMonomers.splice(idx, 1);
+                    this.renderTags();
+                    this.updateCountLabel();
+                }
+            });
+            removeBtn.style.marginLeft = '4px';
+            removeBtn.style.cursor = 'pointer';
+            const tag = ui.div([ui.span([symbol]), removeBtn], {
+                style: {
+                    display: 'inline-flex', alignItems: 'center',
+                    padding: '2px 6px', borderRadius: '4px',
+                    backgroundColor: 'var(--grey-2)', border: '1px solid var(--grey-3)',
+                    fontSize: '12px', cursor: 'default',
+                },
+            });
+            // Tooltip on hover
+            tag.addEventListener('mouseenter', () => {
+                const tooltip = this.monomerLib.getTooltip(this.helmType, symbol);
+                ui.tooltip.show(tooltip, tag.getBoundingClientRect().left, tag.getBoundingClientRect().bottom + 16);
+            });
+            tag.addEventListener('mouseleave', () => { ui.tooltip.hide(); });
+            this.tagsHost.appendChild(tag);
+        }
+        this.updateCountLabel();
+    }
+    addMonomer(symbol) {
+        if (!this.selectedMonomers.includes(symbol)) {
+            this.selectedMonomers.push(symbol);
+            this.renderTags();
+        }
+        this.inputEl.value = '';
+        this.hideMenu();
+        this.inputEl.focus();
+    }
+    addMonomers(symbols) {
+        let added = false;
+        for (const symbol of symbols) {
+            if (!this.selectedMonomers.includes(symbol)) {
+                this.selectedMonomers.push(symbol);
+                added = true;
+            }
+        }
+        if (added)
+            this.renderTags();
+    }
+    hideMenu() {
+        if (this.currentMenu) {
+            this.currentMenu.hide();
+            this.currentMenu = null;
+        }
+        this.menuItems = [];
+        this.highlightedIndex = -1;
+    }
+    getSuggestions(query) {
+        const q = query.toLowerCase();
+        const results = [];
+        for (const symbol of this.allSymbols) {
+            if (this.selectedMonomers.includes(symbol))
+                continue;
+            const monomer = this.monomerLib.getMonomer(this.polymerType, symbol);
+            const symLower = symbol.toLowerCase();
+            const nameLower = monomer?.name?.toLowerCase() ?? '';
+            if (symLower.startsWith(q))
+                results.push({ symbol, monomer, rank: 0 });
+            else if (symLower.includes(q))
+                results.push({ symbol, monomer, rank: 1 });
+            else if (nameLower.includes(q))
+                results.push({ symbol, monomer, rank: 2 });
+        }
+        results.sort((a, b) => a.rank - b.rank || a.symbol.localeCompare(b.symbol));
+        return results.slice(0, MAX_SUGGESTIONS);
+    }
+    showSuggestions() {
+        this.hideMenu();
+        const query = this.inputEl.value.trim();
+        if (!query)
+            return;
+        const suggestions = this.getSuggestions(query);
+        if (suggestions.length === 0)
+            return;
+        this.currentMenu = DG.Menu.popup();
+        const maxElement = suggestions.reduce((max, s) => {
+            const label = s.monomer?.name ? `${s.symbol} - ${s.monomer.name}` : s.symbol;
+            if (max.length < label.length)
+                return label;
+            return max;
+        }, '');
+        this.currentMenu.item(maxElement, () => { }); // Dummy item to set menu width
+        const causedBy = new MouseEvent('mousemove', { clientX: this.inputEl.getBoundingClientRect().left, clientY: this.inputEl.getBoundingClientRect().bottom });
+        this.currentMenu.show({ causedBy: causedBy,
+            y: this.inputEl.offsetHeight + this.inputEl.offsetTop, x: this.inputEl.offsetLeft });
+        // collect menu items for keyboard navigation
+        setTimeout(() => {
+            this.currentMenu?.clear();
+            for (const s of suggestions) {
+                const label = s.monomer?.name ? `${s.symbol} - ${s.monomer.name}` : s.symbol;
+                this.currentMenu?.item(label, () => { this.addMonomer(s.symbol); });
+            }
+            const menuRoot = document.querySelector('.d4-menu-popup:last-of-type');
+            if (menuRoot)
+                this.menuItems = Array.from(menuRoot.querySelectorAll('.d4-menu-item'));
+            this.highlightedIndex = -1;
+        }, 0);
+    }
+    updateHighlight(newIndex) {
+        if (this.menuItems.length === 0)
+            return;
+        if (this.highlightedIndex >= 0 && this.highlightedIndex < this.menuItems.length)
+            this.menuItems[this.highlightedIndex].classList.remove('d4-menu-item-hover');
+        this.highlightedIndex = newIndex;
+        if (this.highlightedIndex >= 0 && this.highlightedIndex < this.menuItems.length) {
+            this.menuItems[this.highlightedIndex].classList.add('d4-menu-item-hover');
+            this.menuItems[this.highlightedIndex].scrollIntoView({ block: 'nearest' });
+        }
+    }
+    setupInputListeners() {
+        this.inputEl.addEventListener('input', () => { this.showSuggestions(); });
+        // Handle pasting multiple monomers (space / comma / newline separated)
+        this.inputEl.addEventListener('paste', (e) => {
+            const pastedText = e.clipboardData?.getData('text');
+            if (!pastedText)
+                return;
+            // Split on newlines first, then parse each line (handles parenthesized symbols like hArg(Et,Et))
+            const lines = pastedText.split(/[\n\r]+/).map((l) => l.trim()).filter((l) => l.length > 0);
+            const candidates = [];
+            for (const line of lines) {
+                const parsed = parseMonomerSymbolList(line);
+                // If parseMonomerSymbolList returned a single token but the line has spaces and no commas,
+                // split on spaces as well (e.g. "K P F" -> ["K", "P", "F"])
+                if (parsed.length === 1 && line.includes(' ') && !line.includes(','))
+                    candidates.push(...line.split(/\s+/).map((s) => s.trim()).filter((s) => s.length > 0));
+                else
+                    candidates.push(...parsed);
+            }
+            if (candidates.length <= 1)
+                return; // Single symbol: let default paste + autocomplete handle it
+            e.preventDefault();
+            for (const candidate of candidates) {
+                if (!this.selectedMonomers.includes(candidate))
+                    this.selectedMonomers.push(candidate);
+            }
+            this.renderTags();
+            this.inputEl.value = '';
+            this.hideMenu();
+            this.inputEl.focus();
+        });
+        this.inputEl.addEventListener('keydown', (e) => {
+            if (e.key === 'ArrowDown') {
+                e.preventDefault();
+                if (this.menuItems.length > 0) {
+                    const next = (this.highlightedIndex + 1) % this.menuItems.length;
+                    this.updateHighlight(next);
+                }
+            }
+            else if (e.key === 'ArrowUp') {
+                e.preventDefault();
+                if (this.menuItems.length > 0) {
+                    const prev = (this.highlightedIndex - 1 + this.menuItems.length) % this.menuItems.length;
+                    this.updateHighlight(prev);
+                }
+            }
+            else if (e.key === 'Enter') {
+                e.preventDefault();
+                e.stopPropagation();
+                if (this.highlightedIndex >= 0 && this.highlightedIndex < this.menuItems.length) {
+                    this.menuItems[this.highlightedIndex].click();
+                }
+                else {
+                    // If input exactly matches a symbol, add it directly
+                    const val = this.inputEl.value.trim();
+                    if (val)
+                        this.addMonomer(val);
+                }
+            }
+            else if (e.key === 'Escape') {
+                this.hideMenu();
+            }
+        });
+    }
+    createLibrarySection() {
+        const librarySection = ui.div([], { style: { marginTop: '8px' } });
+        if (!this.libHelper)
+            return librarySection;
+        const libHelper = this.libHelper;
+        const libraryInput = ui.input.choice('Add from library', { items: [], nullable: true });
+        const libraryStatus = ui.divText('', { style: { fontSize: '11px', color: 'var(--green-2)', marginLeft: '8px', minHeight: '16px' } });
+        libHelper.getAvaliableLibraryNames().then((libNames) => {
+            libraryInput.items = libNames;
+        });
+        libraryInput.onChanged.subscribe(async () => {
+            const libName = libraryInput.value;
+            if (!libName)
+                return;
+            libraryStatus.textContent = 'Loading...';
+            try {
+                const lib = await libHelper.readSingleLibraryByName(libName);
+                if (lib) {
+                    const symbols = lib.getMonomerSymbolsByType(this.polymerType);
+                    const before = this.selectedMonomers.length;
+                    this.addMonomers(symbols);
+                    const added = this.selectedMonomers.length - before;
+                    libraryStatus.textContent = `Added ${added} monomer(s) from "${libName}"`;
+                }
+                else {
+                    libraryStatus.textContent = `Library "${libName}" not found`;
+                }
+            }
+            catch (err) {
+                libraryStatus.textContent = `Error loading library`;
+            }
+            libraryInput.value = null;
+            setTimeout(() => { libraryStatus.textContent = ''; }, 4000);
+        });
+        librarySection.appendChild(ui.divV([libraryInput.root, libraryStatus]));
+        return librarySection;
+    }
+    createCollectionSection() {
+        const collectionSection = ui.div([], { style: { marginTop: '4px' } });
+        if (!this.libHelper)
+            return collectionSection;
+        const libHelper = this.libHelper;
+        const collectionInput = ui.input.choice('Add from collection', { items: [], nullable: true });
+        const collectionStatus = ui.divText('', { style: { fontSize: '11px', color: 'var(--green-2)', marginLeft: '8px', minHeight: '16px' } });
+        libHelper.listMonomerCollections().then((collectionNames) => {
+            collectionInput.items = collectionNames;
+        });
+        collectionInput.onChanged.subscribe(async () => {
+            const collectionName = collectionInput.value;
+            if (!collectionName)
+                return;
+            collectionStatus.textContent = 'Loading...';
+            try {
+                const collection = await libHelper.readMonomerCollection(collectionName);
+                const symbols = collection.monomerSymbols ?? [];
+                const before = this.selectedMonomers.length;
+                this.addMonomers(symbols);
+                const added = this.selectedMonomers.length - before;
+                const displayName = collectionName.replace(/\.json$/, '');
+                collectionStatus.textContent = `Added ${added} monomer(s) from "${displayName}"`;
+            }
+            catch (err) {
+                collectionStatus.textContent = `Error loading collection`;
+            }
+            collectionInput.value = null;
+            setTimeout(() => { collectionStatus.textContent = ''; }, 4000);
+        });
+        collectionSection.appendChild(ui.divV([collectionInput.root, collectionStatus]));
+        return collectionSection;
+    }
+}
+/** Shows a dialog for selecting monomers with autocomplete, tag-based display,
+ * and bulk-add from monomer libraries or collections.
+ * @returns monomer symbols array, or null if cancelled */
+export async function showMonomerSelectionDialog(monomerLib, polymerType, presetMonomers, libHelper) {
+    return new Promise((resolve) => {
+        const widget = new MonomerSelectionWidget(monomerLib, polymerType, presetMonomers, libHelper);
+        const _dlg = ui.dialog({ title: 'Select Monomers', showFooter: true })
+            .add(ui.div([widget.root], { style: { minWidth: '400px', minHeight: '250px', maxWidth: '800px' } }))
+            .onOK(() => { resolve(widget.getSelectedMonomers()); })
+            .onCancel(() => { resolve(null); })
+            .show({ resizable: true });
+        widget.focus();
+    });
+}
+//# sourceMappingURL=monomer-selection-dialog.js.map

package/src/utils/monomer-selection-dialog.js.map

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