@datagrok/helm 3.0.4 → 3.0.6

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Files changed (22) hide show
  1. package/CHANGELOG.md +11 -0
  2. package/dist/489.js +1 -1
  3. package/dist/489.js.map +1 -1
  4. package/dist/package-test.js +1 -1
  5. package/dist/package-test.js.map +1 -1
  6. package/dist/package.js +1 -1
  7. package/dist/package.js.map +1 -1
  8. package/package.json +11 -2
  9. package/src/constants.ts +12 -0
  10. package/src/package-api.ts +8 -0
  11. package/src/package-test.ts +1 -0
  12. package/src/package-utils.ts +37 -0
  13. package/src/package.g.ts +9 -0
  14. package/src/package.ts +20 -0
  15. package/src/tests/helm-input-tests.ts +31 -0
  16. package/src/tests/wrap-width-tests.ts +132 -0
  17. package/src/utils/wrap-width.ts +18 -0
  18. package/src/widgets/helm-input.ts +4 -1
  19. package/src/widgets/wrap-width-widget.ts +73 -0
  20. package/test-console-output-1.log +138 -104
  21. package/test-playwright-report.json +20 -20
  22. package/test-record-1.mp4 +0 -0
package/dist/package.js CHANGED
@@ -1,2 +1,2 @@
1
- var helm;(()=>{var e={130(e,t,i){"use strict";i.d(t,{A:()=>a});var n=i(354),o=i.n(n),r=i(314),s=i.n(r)()(o());s.push([e.id,'/* T-0609 / Phase 19 (T-1902) / Phase 28 (T-2801, T-2804) --\n * Default editor stylesheet. SINGLE source of truth.\n *\n * Build pipeline:\n * 1. tsup copies this file byte-for-byte to `dist/editor.css`\n * (see `tsup.config.ts` -- onSuccess hook).\n * 2. `package.json#exports."./styles.css"` maps the public import\n * `@datagrok-libraries/hwe/styles.css` to `dist/editor.css`, so\n * library consumers do `import \'@datagrok-libraries/hwe/styles.css\';`\n * via their bundler (vite, webpack, rollup, etc.).\n * 3. apps/demo imports this file directly with a relative path\n * (`import \'../../../src/editor/styles/editor.css\';` in main.ts)\n * so vite serves source CSS in dev and bundles it in prod.\n *\n * Phase 28 removed the previous runtime injection path\n * (`injectAppStyles` + `editor-css.generated.ts` TS mirror). Reason:\n * dual delivery was a recurring drift hazard. The bundler is now the\n * SINGLE CSS-delivery channel; tests use `mountEditorCss` (in\n * `tests/helpers/load-css.ts`) to read this file directly when\n * stylesheet-text or `getComputedStyle` checks are needed in linkedom.\n */\n\n.hw-app {\n --hw-bg: #ffffff;\n --hw-fg: #1a1a1a;\n --hw-muted: #6c757d;\n --hw-accent: #1f5fcd;\n --hw-selection: #FFD29B;\n --hw-border: #d8d8d8;\n --hw-border-subtle: #e9ecef;\n --hw-tile-hover: #f1f3f5;\n --hw-toolbar-bg: #f4f5f7;\n --hw-pane-bg: #fafbfc;\n --hw-error: #cc0000;\n /* T-3517 -- toolbar icon stroke colour. Datagrok-style neutral grey\n (icons read as quiet chrome until hovered, then darken to --hw-fg). */\n --hw-icon: #6b7178;\n display: flex;\n flex-direction: column;\n width: 100%;\n height: 100%;\n background: var(--hw-bg);\n color: var(--hw-fg);\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 13px;\n box-sizing: border-box;\n}\n.hw-app--dark {\n --hw-bg: #1a1d23;\n --hw-fg: #e0e0e0;\n --hw-muted: #9aa1a8;\n --hw-accent: #6699ff;\n --hw-selection: #FFD29B;\n --hw-border: #3a3f47;\n --hw-border-subtle: #2c3037;\n --hw-tile-hover: #262a31;\n --hw-toolbar-bg: #22252b;\n --hw-pane-bg: #1f2228;\n --hw-error: #ff5050;\n --hw-icon: #9aa1a8;\n}\n.hw-app *, .hw-app *::before, .hw-app *::after { box-sizing: border-box; }\n\n.hw-app__toolbar { flex: 0 0 auto; }\n.hw-app__main {\n flex: 1 1 auto;\n display: flex;\n flex-direction: row;\n min-height: 0;\n border-top: 1px solid var(--hw-border);\n}\n.hw-app__palette {\n flex: 0 0 220px;\n border-right: 1px solid var(--hw-border);\n overflow: auto;\n background: var(--hw-pane-bg);\n}\n.hw-app__canvas { flex: 1 1 auto; position: relative; min-width: 0; overflow: hidden; }\n.hw-app__panes { flex: 0 0 auto; border-top: 1px solid var(--hw-border); }\n.hw-app__tabs { display: flex; flex-direction: row; background: var(--hw-toolbar-bg); }\n.hw-app__tab {\n padding: 6px 14px;\n cursor: pointer;\n border: none;\n background: transparent;\n color: var(--hw-fg);\n border-right: 1px solid var(--hw-border);\n font-size: 12px;\n}\n.hw-app__tab--active { background: var(--hw-bg); border-bottom: 2px solid var(--hw-accent); }\n/* Cap the active pane\'s height; taller content scrolls within the pane. */\n.hw-app__pane-body { padding: 8px; min-height: 80px; max-height: 300px; overflow: auto; background: var(--hw-bg); }\n\n.hw-toolbar {\n display: flex;\n flex-direction: row;\n align-items: center;\n gap: 4px;\n padding: 4px 6px;\n background: var(--hw-toolbar-bg);\n}\n.hw-toolbar__btn {\n /* T-3517 -- Datagrok-style flat, borderless icon buttons. The icon\n stroke uses the neutral grey --hw-icon; hover darkens it to --hw-fg\n and adds a soft rounded background, matching Datagrok\'s toolbar. */\n border: 1px solid transparent;\n background: transparent;\n color: var(--hw-icon);\n border-radius: 4px;\n padding: 5px;\n cursor: pointer;\n font-size: 13px;\n width: 30px;\n height: 30px;\n display: inline-flex;\n align-items: center;\n justify-content: center;\n transition: background 120ms, color 120ms;\n}\n.hw-toolbar__btn-icon {\n display: inline-block;\n width: 100%;\n height: 100%;\n color: inherit;\n}\n.hw-toolbar__btn-icon > svg {\n width: 100%;\n height: 100%;\n display: block;\n}\n.hw-toolbar__btn:hover { background: var(--hw-tile-hover, var(--hw-toolbar-bg)); color: var(--hw-fg); }\n.hw-toolbar__btn[disabled] { opacity: 0.4; cursor: default; }\n.hw-toolbar__btn--active {\n border-color: var(--hw-accent);\n background: var(--hw-accent);\n color: #ffffff;\n}\n.hw-toolbar__separator {\n display: inline-block;\n width: 1px;\n height: 18px;\n background: var(--hw-border);\n margin: 0 4px;\n}\n\n.hw-palette {\n display: flex;\n flex-direction: column;\n height: 100%;\n padding: 4px;\n}\n.hw-palette__search {\n width: 100%;\n padding: 4px;\n margin-bottom: 6px;\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n background: var(--hw-bg);\n color: var(--hw-fg);\n font-size: 12px;\n flex: 0 0 auto;\n}\n/* T-1421 / T-1423 -- tab list: horizontal row above the panes. Active\n tab gets a 2 px accent underline that absorbs the 1 px container\n border below via a negative bottom margin so the layout does not\n shift when the active tab changes.\n\n Phase 24 (T-2404): when a library exposes many polymer types\n (Favorites + PEPTIDE + RNA + CHEM + BLOB + G = 6 tabs), they can no\n longer fit horizontally inside the 200 px palette pane and the\n browser shows an unobvious horizontal scrollbar. Switch to\n `flex-wrap: wrap` so overflow tabs wrap onto a second (or third)\n row -- no hidden scrollbar, every tab is always visible. The\n per-tab padding shrinks too so more tabs fit per row before\n wrapping. */\n.hw-palette__tabs {\n display: flex;\n flex-wrap: wrap;\n gap: 2px 4px;\n border-bottom: 1px solid var(--hw-border);\n flex: 0 0 auto;\n /* Defensively: no overflow scrolling -- wrapping is the answer. */\n overflow: hidden;\n}\n.hw-palette__tab {\n /* Phase 24 (T-2404): compact padding + min-width so 6 tabs still fit\n in two rows max within a 200 px palette pane. */\n flex: 0 0 auto;\n padding: 6px 8px;\n cursor: pointer;\n border: none;\n background: transparent;\n font-size: 12px;\n color: var(--hw-muted);\n user-select: none;\n white-space: nowrap;\n min-width: 0;\n}\n.hw-palette__tab:hover {\n color: var(--hw-fg);\n background: var(--hw-tile-hover);\n}\n.hw-palette__tab[aria-selected="true"] {\n color: var(--hw-fg);\n border-bottom: 2px solid var(--hw-accent);\n margin-bottom: -1px;\n font-weight: 600;\n}\n.hw-palette__panes {\n flex: 1 1 auto;\n min-height: 0;\n}\n.hw-palette__pane {\n overflow-y: auto;\n max-height: 100%;\n padding: 4px 6px;\n}\n.hw-palette__pane[hidden] { display: none; }\n.hw-palette__placeholder {\n padding: 12px 6px;\n color: var(--hw-muted);\n font-size: 12px;\n font-style: italic;\n}\n/* T-1423 -- bolder, more separated group headers. */\n.hw-palette__group { margin-bottom: 12px; }\n.hw-palette__group-header {\n font-size: 13px;\n font-weight: 700;\n color: var(--hw-muted);\n padding: 8px 4px 4px;\n margin: 8px 0 4px;\n border-bottom: 1px solid var(--hw-border-subtle);\n text-transform: uppercase;\n letter-spacing: 0.04em;\n}\n.hw-palette__group-tiles {\n display: grid;\n grid-template-columns: repeat(3, 1fr);\n gap: 6px;\n padding: 2px;\n}\n.hw-palette__tiles { display: flex; flex-wrap: wrap; gap: 6px; padding: 2px; }\n.hw-palette__tile {\n position: relative;\n display: flex;\n flex-direction: column;\n align-items: center;\n justify-content: center;\n width: 100%;\n min-width: 48px;\n max-width: none;\n height: 40px;\n padding: 4px 6px;\n border: 2px solid var(--hw-border);\n border-radius: 8px;\n background: #ffffff;\n cursor: grab;\n font-size: 13px;\n font-weight: 600;\n user-select: none;\n overflow: hidden;\n text-overflow: ellipsis;\n box-shadow: 0 1px 2px rgba(0, 0, 0, 0.08);\n transition: border-color 120ms, transform 120ms, box-shadow 120ms;\n box-sizing: border-box;\n}\n.hw-palette__tile:hover {\n border-color: var(--hw-accent);\n transform: translateY(-1px);\n box-shadow: 0 2px 4px rgba(0, 0, 0, 0.12);\n}\n.hw-palette__tile[aria-pressed="true"],\n.hw-palette__tile--primed {\n border-color: var(--hw-accent);\n box-shadow: 0 0 0 2px rgba(31, 95, 205, 0.18);\n}\n.hw-palette__tile--favorite { outline: 1px dashed var(--hw-accent); outline-offset: -3px; }\n.hw-palette__tile--low-contrast {\n box-shadow: inset 0 0 0 1px rgba(0, 0, 0, 0.4), 0 1px 2px rgba(0, 0, 0, 0.08);\n}\n.hw-palette__star {\n position: absolute;\n top: 2px;\n right: 4px;\n font-size: 10px;\n cursor: pointer;\n color: var(--hw-muted);\n}\n.hw-palette__tile--favorite .hw-palette__star { color: var(--hw-accent); }\n.hw-palette__label {\n font-weight: 600;\n letter-spacing: 0.02em;\n display: inline-block;\n max-width: 80px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n}\n\n/* Phase 18 (T-1806) / Phase 19 (T-1903) / Phase 20 (T-2002) -- RNA Builder.\n Phase 20 redesign: SVG triplet visualization. Sugar (square),\n linker (circle), base (diamond) -- each clickable to enter pick\n mode. Fills come from the resolved monomer colour palette so the\n preview matches the canvas rendering. */\n.hw-rna-builder {\n display: block;\n /* Phase 21 (T-2101): horizontal margin nudges the builder rightward\n so it visually aligns with the palette tile column below. The\n user reported the SVG sat too far left vs. the tile rows. */\n margin: 4px 8px 12px;\n padding: 8px;\n background: var(--hw-pane-bg, #fafbfc);\n border: 1px solid var(--hw-border-subtle, #e9ecef);\n border-radius: 6px;\n}\n/* T-3513 -- header row holds the title plus the favorite star. */\n.hw-rna-builder__header {\n display: flex;\n align-items: center;\n justify-content: space-between;\n margin-bottom: 6px;\n}\n.hw-rna-builder__title {\n font-weight: 700;\n font-size: 12px;\n color: var(--hw-muted);\n text-transform: uppercase;\n letter-spacing: 0.04em;\n}\n.hw-rna-builder__header .hw-rna-builder__title {\n margin-bottom: 0;\n}\n/* T-3513 -- favorite star toggling the composed triplet. */\n.hw-rna-builder__fav {\n font-size: 15px;\n line-height: 1;\n cursor: pointer;\n color: var(--hw-muted);\n user-select: none;\n}\n.hw-rna-builder__fav--active { color: var(--hw-accent); }\n.hw-rna-builder__fav--disabled { opacity: 0.35; cursor: default; }\n/* Phase 29 (T-2901) -- Pick-mode hint shown directly under the "RNA\n builder" title while a slot is in pick mode. Replaces the Phase 24\n palette-level reserved-space hint above the search box. The hint\n carries the `hidden` HTML attribute when idle so the SVG triplet\n sits flush against the title (no wasted vertical space). User\n request 2026-05-19: "lets not have that empty space, and just\n display that text in bold below \'RNA BUILDER\' header, inside the\n builder itself." */\n.hw-rna-builder__hint {\n font-weight: 700;\n font-size: 12px;\n color: var(--hw-accent);\n margin: 4px 0 -14px;\n}\n.hw-rna-builder__hint[hidden] {\n display: none;\n}\n.hw-rna-builder__triplet {\n display: block;\n width: 100%;\n max-width: 180px;\n height: auto;\n max-height: 10vh;\n margin: 0 auto 6px;\n}\n.hw-rna-builder__bond {\n stroke: var(--hw-fg, #1a1a1a);\n stroke-width: 1.5;\n fill: none;\n}\n.hw-rna-builder__slot {\n cursor: pointer;\n}\n.hw-rna-builder__slot-shape {\n stroke-width: 1.5;\n transition: filter 120ms;\n}\n.hw-rna-builder__slot:hover .hw-rna-builder__slot-shape {\n filter: brightness(1.08);\n stroke-width: 2.5;\n}\n.hw-rna-builder__slot-label {\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n /* Phase 21 (T-2102): font-size is set per-label inline via\n setAttribute(\'font-size\', ...) so a long symbol like `[5meC]`\n can scale down. The CSS default below is a safety net for\n pre-T-2102 markup. */\n font-size: 12px;\n font-weight: 700;\n user-select: none;\n pointer-events: none;\n}\n.hw-rna-builder__slot--active .hw-rna-builder__slot-shape,\n.hw-rna-builder__slot[aria-pressed="true"] .hw-rna-builder__slot-shape {\n /* Yellow halo via filter so per-monomer fill / stroke stays intact. */\n filter: drop-shadow(0 0 3px #ffeb3b) drop-shadow(0 0 2px #ffeb3b);\n stroke-width: 2.5;\n}\n.hw-rna-builder__slot:focus {\n outline: none;\n}\n.hw-rna-builder__slot:focus-visible .hw-rna-builder__slot-shape {\n stroke: var(--hw-accent);\n stroke-width: 2.5;\n}\n.hw-rna-builder__preview {\n margin: 6px 0;\n font-size: 11px;\n color: var(--hw-fg);\n font-family: ui-monospace, Menlo, Consolas, monospace;\n text-align: center;\n}\n.hw-rna-builder__add {\n display: block;\n width: 100%;\n padding: 4px 8px;\n background: var(--hw-accent);\n color: #ffffff;\n border: 1px solid var(--hw-accent);\n border-radius: 3px;\n font-size: 12px;\n font-weight: 600;\n cursor: pointer;\n}\n.hw-rna-builder__add:hover { opacity: 0.9; }\n.hw-rna-builder__add:active { transform: translateY(1px); }\n\n/* T-3513 -- RNA triplet chips. Small, monospace, wrap into a tight row.\n Used by the RNA pane\'s default-nucleotide row (r(A)p ... r(T)p) and by\n triplet favorites in the Favorites pane. Kept compact because the RNA\n pane\'s vertical space is constrained by the RNA builder above it. */\n.hw-triplet-chips {\n display: flex;\n flex-wrap: wrap;\n gap: 4px;\n padding: 2px;\n}\n.hw-triplet-chips--defaults {\n margin: 0 0 8px;\n}\n.hw-triplet-chip {\n position: relative;\n display: inline-flex;\n align-items: center;\n gap: 2px;\n height: 22px;\n padding: 0 6px;\n border: 1px solid var(--hw-border);\n border-radius: 11px;\n font-family: ui-monospace, Menlo, Consolas, monospace;\n font-size: 11px;\n font-weight: 600;\n line-height: 1;\n cursor: pointer;\n user-select: none;\n box-shadow: 0 1px 1px rgba(0, 0, 0, 0.08);\n transition: border-color 120ms, transform 120ms;\n}\n.hw-triplet-chip:hover {\n border-color: var(--hw-accent);\n transform: translateY(-1px);\n}\n.hw-triplet-chip--favorite { border-color: var(--hw-accent); }\n.hw-triplet-chip__star {\n font-size: 10px;\n cursor: pointer;\n color: var(--hw-muted);\n}\n.hw-triplet-chip--favorite .hw-triplet-chip__star { color: var(--hw-accent); }\n.hw-triplet-chip__label { letter-spacing: 0.02em; }\n\n/* Phase 29 (T-2901) -- The Phase 24 palette-level pick-mode hint\n container has been REMOVED. The hint now lives inside the RNA\n Builder as `.hw-rna-builder__hint` (see the rules under the RNA\n Builder block above). The user explicitly reported the\n reserved-space hint above the search box as "wasted space". */\n\n.hw-pane { display: block; }\n.hw-pane__content { font-family: ui-monospace, Menlo, Consolas, monospace; font-size: 12px; white-space: pre-wrap; word-break: break-all; }\n.hw-pane__notation {\n outline: none;\n border: 1px solid var(--hw-border);\n padding: 4px;\n background: var(--hw-bg);\n}\n.hw-pane__error { color: var(--hw-error); font-size: 11px; margin-top: 4px; display: none; }\n.hw-pane__error--visible { display: block; }\n.hw-pane__prop-row { display: flex; gap: 8px; padding: 2px 0; }\n.hw-pane__prop-label { color: var(--hw-muted); width: 180px; }\n.hw-pane__prop-value { color: var(--hw-fg); }\n.hw-pane__placeholder { color: var(--hw-muted); font-style: italic; }\n\n.hw-pane__content.hw-pane__sequence, .hw-pane__content.hw-pane__notation {\n max-height: 100px;\n overflow: scroll;\n}\n\n.hw-modal-backdrop {\n position: absolute;\n top: 0; left: 0; right: 0; bottom: 0;\n background: rgba(0,0,0,0.3);\n display: flex; align-items: center; justify-content: center;\n z-index: 1000;\n}\n.hw-modal {\n background: var(--hw-bg);\n color: var(--hw-fg);\n border: 1px solid var(--hw-border);\n border-radius: 4px;\n min-width: 320px;\n max-width: 600px;\n padding: 12px;\n}\n.hw-modal__header { font-weight: bold; padding-bottom: 8px; border-bottom: 1px solid var(--hw-border); }\n.hw-modal__body { padding-top: 8px; }\n.hw-modal__row { display: flex; gap: 8px; align-items: center; padding: 4px 0; }\n.hw-modal__label { color: var(--hw-fg); min-width: 100px; }\n.hw-modal__input, .hw-modal__select {\n flex: 1;\n padding: 4px;\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n background: var(--hw-bg);\n color: var(--hw-fg);\n}\n.hw-modal__check { transform: scale(1.1); }\n.hw-modal__actions { display: flex; justify-content: flex-end; gap: 6px; padding-top: 10px; }\n.hw-modal__ok, .hw-modal__cancel, .hw-modal__find-next, .hw-modal__replace, .hw-modal__replace-all {\n padding: 4px 10px;\n border: 1px solid var(--hw-border);\n background: var(--hw-bg);\n color: var(--hw-fg);\n border-radius: 3px;\n cursor: pointer;\n}\n.hw-modal__ok { background: var(--hw-accent); color: #ffffff; border-color: var(--hw-accent); }\n.hw-modal__result { color: var(--hw-muted); font-size: 11px; padding-top: 6px; }\n\n/* Phase 23 (T-2304) -- Bond editor endpoint preview row. Renders two\n monomer structures (atom A1 and atom A2) flanking a `↔` arrow so the\n user can see what they\'re connecting while picking R-groups. The\n SVG inside each cell stretches via the .hw-bond-props__atom-rdkit\n svg rule below (matches the tooltip pattern). */\n.hw-bond-props__atoms {\n display: flex;\n align-items: center;\n gap: 16px;\n margin: 12px 0;\n}\n.hw-bond-props__atom {\n flex: 1;\n text-align: center;\n}\n.hw-bond-props__atom-label {\n font-weight: 600;\n margin-bottom: 6px;\n color: var(--hw-fg);\n}\n.hw-bond-props__atom-rdkit {\n width: 180px;\n height: 120px;\n margin: 0 auto 8px;\n background: #fafafa;\n border: 1px solid #f3f4f6;\n border-radius: 4px;\n padding: 4px;\n box-sizing: border-box;\n}\n.hw-bond-props__atom-rdkit svg {\n display: block;\n width: 100%;\n height: 100%;\n}\n.hw-bond-props__bond-arrow {\n font-size: 24px;\n color: var(--hw-muted);\n flex: 0 0 auto;\n}\n\n.hw-editor-view {\n width: 100%;\n height: 100%;\n position: relative;\n --hw-hover: #ff8c00;\n}\n.hw-editor-view svg { width: 100%; height: 100%; }\n\n/* T-1103 / Phase 19 (T-1901) -- Cursor affordance only. We removed\n the :hover rules that recoloured the atom\'s own outline because\n they ran in PARALLEL with the real highlight ring painted by the\n renderer (teal #26A69A), producing the wrong colour the user\n reported as "yellow on hover" (the CSS rule re-stroked the atom in\n var(--hw-hover) = #ff8c00, an orange-yellow). The renderer\'s\n highlight layer is now the single source of truth for hover\n feedback. */\n.hw-atom { cursor: pointer; }\n.hw-bond { cursor: pointer; }\n\n/* Mode-specific cursors on the canvas wrapper. The editor adds an\n hw-editor-view--<mode> class via the option:change handler. */\n.hw-editor-view--select svg { cursor: default; }\n.hw-editor-view--eraser svg { cursor: not-allowed; }\n.hw-editor-view--hbond svg { cursor: crosshair; }\n.hw-editor-view--move svg { cursor: grab; }\n.hw-editor-view--move:active svg { cursor: grabbing; }\n\n/* Phase 22 (T-2201) -- Unified tooltip styling. Three tooltip variants\n share the same look-and-feel: atom hover (canvas), bond hover\n (canvas), palette-tile hover (left pane), and rna-builder slot hover.\n Pre-Phase 22 the tooltips were absolutely-positioned, dark, and\n z-index 100 -- the gallery panel (z-index higher) ate into them and\n the dark background looked heavy. Phase 22 mounts the tooltip at\n `document.body` (escaping every parent stacking context), pins\n `z-index: 99999`, and paints them white with a soft drop shadow and\n darker body text so they read clearly over any backdrop. */\n/* Phase 32 (T-3003) -- Ghost cursor preview that follows the mouse\n when a palette tile is primed in select mode. `pointer-events:\n none` so the underlying canvas keeps receiving clicks / drags. The\n z-index sits just below the tooltips (99998 vs 99999) so a real\n tooltip can still overlay the ghost if both happen to be visible. */\n.hw-next-add-cursor {\n position: fixed;\n pointer-events: none;\n z-index: 99998;\n opacity: 0.7;\n display: none;\n}\n.hw-next-add-cursor__svg {\n display: block;\n}\n\n.hw-atom-tooltip,\n.hw-bond-tooltip,\n.hw-palette-tooltip,\n.hw-builder-tooltip,\n.hw-toolbar-tooltip {\n position: fixed;\n pointer-events: none;\n background: #ffffff;\n color: #1f2937;\n border: 1px solid #e5e7eb;\n border-radius: 6px;\n box-shadow: 0 4px 16px rgba(0, 0, 0, 0.12), 0 2px 4px rgba(0, 0, 0, 0.08);\n padding: 10px 12px;\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 12px;\n line-height: 1.4;\n max-width: 240px;\n z-index: 99999;\n}\n/* T-3516 -- toolbar button tooltip: a single compact line, no wrap. */\n.hw-toolbar-tooltip {\n padding: 5px 8px;\n white-space: nowrap;\n font-weight: 500;\n}\n.hw-tooltip__symbol {\n font-weight: 700;\n color: #111827;\n}\n/* T-3514 -- RNA triplet tooltip: three monomer structures side by side.\n Wider than the single-structure tooltip so all three columns fit. */\n.hw-triplet-tooltip { max-width: 420px; }\n.hw-tooltip__triplet {\n display: flex;\n gap: 8px;\n margin-top: 6px;\n}\n.hw-tooltip__triplet-part {\n flex: 1 1 0;\n min-width: 0;\n text-align: center;\n}\n.hw-tooltip__triplet-role {\n font-weight: 600;\n color: #111827;\n font-size: 11px;\n}\n.hw-tooltip__name {\n color: #4b5563;\n}\n.hw-tooltip__hint {\n color: #6b7280;\n font-style: italic;\n font-size: 11px;\n margin-top: 6px;\n}\n.hw-tooltip__rdkit {\n display: block;\n margin-top: 8px;\n /* padding-top: 8px; */\n border-top: 1px solid #f3f4f6;\n background: #fafafa;\n border-radius: 4px;\n}\n/* Phase 23 (T-2303) -- The user reported "molecules do not take the full\n space" in the tooltip. RDKit emits an svg with a `viewBox`, so\n `width: 100%; height: auto` lets the structure stretch responsively\n to whatever width the parent tooltip column has. `max-height` caps\n tall structures so they never blow up the tooltip vertically. */\n.hw-tooltip__rdkit svg,\n[data-testid="atom-tooltip-rdkit-svg"] svg,\n[data-testid="palette-tooltip-rdkit-svg"] svg,\n[data-testid="builder-tooltip-rdkit-svg"] svg {\n display: block;\n width: 100%;\n height: auto;\n max-height: 180px;\n margin: 0 auto;\n}\n/* Legacy aliases (kept so Phase 21 atom-tooltip text styling still\n resolves). The body text colour is now driven by the parent tooltip\n rule above; the legacy classes keep the line-wrap behaviour. */\n.hw-atom-tooltip__text {\n display: block;\n}\n\n/* Status indicator (T-1106) -- small badge in the bottom-left of the canvas. */\n.hw-status-bar {\n position: absolute;\n left: 6px;\n bottom: 6px;\n padding: 2px 8px;\n background: rgba(255, 255, 255, 0.85);\n color: var(--hw-fg);\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n font-size: 11px;\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n pointer-events: none;\n z-index: 50;\n}\n.hw-app--dark .hw-status-bar { background: rgba(34, 36, 41, 0.85); }\n\n.hw-status-bar__mode {\n display: inline-flex;\n align-items: center;\n gap: 0;\n}\n.hw-status-bar__message {\n display: inline-block;\n margin-left: 8px;\n font-weight: 500;\n}\n.hw-status-bar__message[data-severity="info"] { color: var(--hw-fg); }\n.hw-status-bar__message[data-severity="warn"] { color: #b8860b; }\n.hw-status-bar__message[data-severity="error"] { color: #c0392b; }\n.hw-app--dark .hw-status-bar__message[data-severity="warn"] { color: #f7c948; }\n.hw-app--dark .hw-status-bar__message[data-severity="error"] { color: #ff6b6b; }\n\n/* Phase 25 (T-2504) -- "Next add: X [x]" clear button. The status bar\n itself sets `pointer-events: none` (it floats above the canvas as a\n non-interactive badge), so the button explicitly re-enables hits on\n itself only. Visible only when `nextAdd` is primed because the\n element is conditionally appended in `_refreshStatus`. */\n.hw-status-bar__next-add-symbol {\n display: inline-block;\n font-weight: 600;\n}\n.hw-status-bar__next-add-clear {\n display: inline-flex;\n align-items: center;\n justify-content: center;\n width: 16px;\n height: 16px;\n margin-left: 6px;\n padding: 0;\n background: transparent;\n border: 1px solid #d1d5db;\n border-radius: 50%;\n color: #6b7280;\n font-size: 12px;\n line-height: 1;\n cursor: pointer;\n pointer-events: auto;\n}\n.hw-status-bar__next-add-clear:hover {\n background: #f3f4f6;\n color: #1f2937;\n border-color: #9ca3af;\n}\n\n.hw-bond-preview { pointer-events: none; opacity: 0.85; }\n\n.hw-help-modal-backdrop {\n position: fixed; left: 0; top: 0; right: 0; bottom: 0;\n background: rgba(0,0,0,0.4);\n display: flex; align-items: center; justify-content: center;\n z-index: 2000;\n}\n.hw-help-modal {\n background: #ffffff;\n color: #1a1a1a;\n padding: 16px 20px;\n 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T-0609 / Phase 19 (T-1902) / Phase 28 (T-2801, T-2804) --\n * Default editor stylesheet. SINGLE source of truth.\n *\n * Build pipeline:\n * 1. tsup copies this file byte-for-byte to `dist/editor.css`\n * (see `tsup.config.ts` -- onSuccess hook).\n * 2. `package.json#exports."./styles.css"` maps the public import\n * `@datagrok-libraries/hwe/styles.css` to `dist/editor.css`, so\n * library consumers do `import \'@datagrok-libraries/hwe/styles.css\';`\n * via their bundler (vite, webpack, rollup, etc.).\n * 3. apps/demo imports this file directly with a relative path\n * (`import \'../../../src/editor/styles/editor.css\';` in main.ts)\n * so vite serves source CSS in dev and bundles it in prod.\n *\n * Phase 28 removed the previous runtime injection path\n * (`injectAppStyles` + `editor-css.generated.ts` TS mirror). Reason:\n * dual delivery was a recurring drift hazard. The bundler is now the\n * SINGLE CSS-delivery channel; tests use `mountEditorCss` (in\n * `tests/helpers/load-css.ts`) to read this file directly when\n * stylesheet-text or `getComputedStyle` checks are needed in linkedom.\n */\n\n.hw-app {\n --hw-bg: #ffffff;\n --hw-fg: #1a1a1a;\n --hw-muted: #6c757d;\n --hw-accent: #1f5fcd;\n --hw-selection: #FFD29B;\n --hw-border: #d8d8d8;\n --hw-border-subtle: #e9ecef;\n --hw-tile-hover: #f1f3f5;\n --hw-toolbar-bg: #f4f5f7;\n --hw-pane-bg: #fafbfc;\n --hw-error: #cc0000;\n /* T-3517 -- toolbar icon stroke colour. Datagrok-style neutral grey\n (icons read as quiet chrome until hovered, then darken to --hw-fg). */\n --hw-icon: #6b7178;\n display: flex;\n flex-direction: column;\n width: 100%;\n height: 100%;\n background: var(--hw-bg);\n color: var(--hw-fg);\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 13px;\n box-sizing: border-box;\n}\n.hw-app--dark {\n --hw-bg: #1a1d23;\n --hw-fg: #e0e0e0;\n --hw-muted: #9aa1a8;\n --hw-accent: #6699ff;\n --hw-selection: #FFD29B;\n --hw-border: #3a3f47;\n --hw-border-subtle: #2c3037;\n --hw-tile-hover: #262a31;\n --hw-toolbar-bg: #22252b;\n --hw-pane-bg: #1f2228;\n --hw-error: #ff5050;\n --hw-icon: #9aa1a8;\n}\n.hw-app *, .hw-app *::before, .hw-app *::after { box-sizing: border-box; }\n\n.hw-app__toolbar { flex: 0 0 auto; }\n.hw-app__main {\n flex: 1 1 auto;\n display: flex;\n flex-direction: row;\n min-height: 0;\n border-top: 1px solid var(--hw-border);\n}\n.hw-app__palette {\n flex: 0 0 220px;\n border-right: 1px solid var(--hw-border);\n overflow: auto;\n background: var(--hw-pane-bg);\n}\n.hw-app__canvas { flex: 1 1 auto; position: relative; min-width: 0; overflow: hidden; }\n.hw-app__panes { flex: 0 0 auto; border-top: 1px solid var(--hw-border); }\n.hw-app__tabs { display: flex; flex-direction: row; background: var(--hw-toolbar-bg); }\n.hw-app__tab {\n padding: 6px 14px;\n cursor: pointer;\n border: none;\n background: transparent;\n color: var(--hw-fg);\n border-right: 1px solid var(--hw-border);\n font-size: 12px;\n}\n.hw-app__tab--active { background: var(--hw-bg); border-bottom: 2px solid var(--hw-accent); }\n/* Cap the active pane\'s height; taller content scrolls within the pane. */\n.hw-app__pane-body { padding: 8px; min-height: 80px; max-height: 300px; overflow: auto; background: var(--hw-bg); }\n\n.hw-toolbar {\n display: flex;\n flex-direction: row;\n align-items: center;\n gap: 4px;\n padding: 4px 6px;\n background: var(--hw-toolbar-bg);\n}\n.hw-toolbar__btn {\n /* T-3517 -- Datagrok-style flat, borderless icon buttons. The icon\n stroke uses the neutral grey --hw-icon; hover darkens it to --hw-fg\n and adds a soft rounded background, matching Datagrok\'s toolbar. */\n border: 1px solid transparent;\n background: transparent;\n color: var(--hw-icon);\n border-radius: 4px;\n padding: 5px;\n cursor: pointer;\n font-size: 13px;\n width: 30px;\n height: 30px;\n display: inline-flex;\n align-items: center;\n justify-content: center;\n transition: background 120ms, color 120ms;\n}\n.hw-toolbar__btn-icon {\n display: inline-block;\n width: 100%;\n height: 100%;\n color: inherit;\n}\n.hw-toolbar__btn-icon > svg {\n width: 100%;\n height: 100%;\n display: block;\n}\n.hw-toolbar__btn:hover { background: var(--hw-tile-hover, var(--hw-toolbar-bg)); color: var(--hw-fg); }\n.hw-toolbar__btn[disabled] { opacity: 0.4; cursor: default; }\n.hw-toolbar__btn--active {\n border-color: var(--hw-accent);\n background: var(--hw-accent);\n color: #ffffff;\n}\n.hw-toolbar__separator {\n display: inline-block;\n width: 1px;\n height: 18px;\n background: var(--hw-border);\n margin: 0 4px;\n}\n\n.hw-palette {\n display: flex;\n flex-direction: column;\n height: 100%;\n padding: 4px;\n}\n.hw-palette__search {\n width: 100%;\n padding: 4px;\n margin-bottom: 6px;\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n background: var(--hw-bg);\n color: var(--hw-fg);\n font-size: 12px;\n flex: 0 0 auto;\n}\n/* T-1421 / T-1423 -- tab list: horizontal row above the panes. Active\n tab gets a 2 px accent underline that absorbs the 1 px container\n border below via a negative bottom margin so the layout does not\n shift when the active tab changes.\n\n Phase 24 (T-2404): when a library exposes many polymer types\n (Favorites + PEPTIDE + RNA + CHEM + BLOB + G = 6 tabs), they can no\n longer fit horizontally inside the 200 px palette pane and the\n browser shows an unobvious horizontal scrollbar. Switch to\n `flex-wrap: wrap` so overflow tabs wrap onto a second (or third)\n row -- no hidden scrollbar, every tab is always visible. The\n per-tab padding shrinks too so more tabs fit per row before\n wrapping. */\n.hw-palette__tabs {\n display: flex;\n flex-wrap: wrap;\n gap: 2px 4px;\n border-bottom: 1px solid var(--hw-border);\n flex: 0 0 auto;\n /* Defensively: no overflow scrolling -- wrapping is the answer. */\n overflow: hidden;\n}\n.hw-palette__tab {\n /* Phase 24 (T-2404): compact padding + min-width so 6 tabs still fit\n in two rows max within a 200 px palette pane. */\n flex: 0 0 auto;\n padding: 6px 8px;\n cursor: pointer;\n border: none;\n background: transparent;\n font-size: 12px;\n color: var(--hw-muted);\n user-select: none;\n white-space: nowrap;\n min-width: 0;\n}\n.hw-palette__tab:hover {\n color: var(--hw-fg);\n background: var(--hw-tile-hover);\n}\n.hw-palette__tab[aria-selected="true"] {\n color: var(--hw-fg);\n border-bottom: 2px solid var(--hw-accent);\n margin-bottom: -1px;\n font-weight: 600;\n}\n.hw-palette__panes {\n flex: 1 1 auto;\n min-height: 0;\n}\n.hw-palette__pane {\n overflow-y: auto;\n max-height: 100%;\n padding: 4px 6px;\n}\n.hw-palette__pane[hidden] { display: none; }\n.hw-palette__placeholder {\n padding: 12px 6px;\n color: var(--hw-muted);\n font-size: 12px;\n font-style: italic;\n}\n/* T-1423 -- bolder, more separated group headers. */\n.hw-palette__group { margin-bottom: 12px; }\n.hw-palette__group-header {\n font-size: 13px;\n font-weight: 700;\n color: var(--hw-muted);\n padding: 8px 4px 4px;\n margin: 8px 0 4px;\n border-bottom: 1px solid var(--hw-border-subtle);\n text-transform: uppercase;\n letter-spacing: 0.04em;\n}\n.hw-palette__group-tiles {\n display: grid;\n grid-template-columns: repeat(3, 1fr);\n gap: 6px;\n padding: 2px;\n}\n.hw-palette__tiles { display: flex; flex-wrap: wrap; gap: 6px; padding: 2px; }\n.hw-palette__tile {\n position: relative;\n display: flex;\n flex-direction: column;\n align-items: center;\n justify-content: center;\n width: 100%;\n min-width: 48px;\n max-width: none;\n height: 40px;\n padding: 4px 6px;\n border: 2px solid var(--hw-border);\n border-radius: 8px;\n background: #ffffff;\n cursor: grab;\n font-size: 13px;\n font-weight: 600;\n user-select: none;\n overflow: hidden;\n text-overflow: ellipsis;\n box-shadow: 0 1px 2px rgba(0, 0, 0, 0.08);\n transition: border-color 120ms, transform 120ms, box-shadow 120ms;\n box-sizing: border-box;\n}\n.hw-palette__tile:hover {\n border-color: var(--hw-accent);\n transform: translateY(-1px);\n box-shadow: 0 2px 4px rgba(0, 0, 0, 0.12);\n}\n.hw-palette__tile[aria-pressed="true"],\n.hw-palette__tile--primed {\n border-color: var(--hw-accent);\n box-shadow: 0 0 0 2px rgba(31, 95, 205, 0.18);\n}\n.hw-palette__tile--favorite { outline: 1px dashed var(--hw-accent); outline-offset: -3px; }\n.hw-palette__tile--low-contrast {\n box-shadow: inset 0 0 0 1px rgba(0, 0, 0, 0.4), 0 1px 2px rgba(0, 0, 0, 0.08);\n}\n.hw-palette__star {\n position: absolute;\n top: 2px;\n right: 4px;\n font-size: 10px;\n cursor: pointer;\n color: var(--hw-muted);\n}\n.hw-palette__tile--favorite .hw-palette__star { color: var(--hw-accent); }\n.hw-palette__label {\n font-weight: 600;\n letter-spacing: 0.02em;\n display: inline-block;\n max-width: 80px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n}\n\n/* Phase 18 (T-1806) / Phase 19 (T-1903) / Phase 20 (T-2002) -- RNA Builder.\n Phase 20 redesign: SVG triplet visualization. Sugar (square),\n linker (circle), base (diamond) -- each clickable to enter pick\n mode. Fills come from the resolved monomer colour palette so the\n preview matches the canvas rendering. */\n.hw-rna-builder {\n display: block;\n /* Phase 21 (T-2101): horizontal margin nudges the builder rightward\n so it visually aligns with the palette tile column below. The\n user reported the SVG sat too far left vs. the tile rows. */\n margin: 4px 8px 12px;\n padding: 8px;\n background: var(--hw-pane-bg, #fafbfc);\n border: 1px solid var(--hw-border-subtle, #e9ecef);\n border-radius: 6px;\n}\n/* T-3513 -- header row holds the title plus the favorite star. */\n.hw-rna-builder__header {\n display: flex;\n align-items: center;\n justify-content: space-between;\n margin-bottom: 6px;\n}\n.hw-rna-builder__title {\n font-weight: 700;\n font-size: 12px;\n color: var(--hw-muted);\n text-transform: uppercase;\n letter-spacing: 0.04em;\n}\n.hw-rna-builder__header .hw-rna-builder__title {\n margin-bottom: 0;\n}\n/* T-3513 -- favorite star toggling the composed triplet. */\n.hw-rna-builder__fav {\n font-size: 15px;\n line-height: 1;\n cursor: pointer;\n color: var(--hw-muted);\n user-select: none;\n}\n.hw-rna-builder__fav--active { color: var(--hw-accent); }\n.hw-rna-builder__fav--disabled { opacity: 0.35; cursor: default; }\n/* Phase 29 (T-2901) -- Pick-mode hint shown directly under the "RNA\n builder" title while a slot is in pick mode. Replaces the Phase 24\n palette-level reserved-space hint above the search box. The hint\n carries the `hidden` HTML attribute when idle so the SVG triplet\n sits flush against the title (no wasted vertical space). User\n request 2026-05-19: "lets not have that empty space, and just\n display that text in bold below \'RNA BUILDER\' header, inside the\n builder itself." */\n.hw-rna-builder__hint {\n font-weight: 700;\n font-size: 12px;\n color: var(--hw-accent);\n margin: 4px 0 -14px;\n}\n.hw-rna-builder__hint[hidden] {\n display: none;\n}\n.hw-rna-builder__triplet {\n display: block;\n width: 100%;\n max-width: 180px;\n height: auto;\n max-height: 10vh;\n margin: 0 auto 6px;\n}\n.hw-rna-builder__bond {\n stroke: var(--hw-fg, #1a1a1a);\n stroke-width: 1.5;\n fill: none;\n}\n.hw-rna-builder__slot {\n cursor: pointer;\n}\n.hw-rna-builder__slot-shape {\n stroke-width: 1.5;\n transition: filter 120ms;\n}\n.hw-rna-builder__slot:hover .hw-rna-builder__slot-shape {\n filter: brightness(1.08);\n stroke-width: 2.5;\n}\n.hw-rna-builder__slot-label {\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n /* Phase 21 (T-2102): font-size is set per-label inline via\n setAttribute(\'font-size\', ...) so a long symbol like `[5meC]`\n can scale down. The CSS default below is a safety net for\n pre-T-2102 markup. */\n font-size: 12px;\n font-weight: 700;\n user-select: none;\n pointer-events: none;\n}\n.hw-rna-builder__slot--active .hw-rna-builder__slot-shape,\n.hw-rna-builder__slot[aria-pressed="true"] .hw-rna-builder__slot-shape {\n /* Yellow halo via filter so per-monomer fill / stroke stays intact. */\n filter: drop-shadow(0 0 3px #ffeb3b) drop-shadow(0 0 2px #ffeb3b);\n stroke-width: 2.5;\n}\n.hw-rna-builder__slot:focus {\n outline: none;\n}\n.hw-rna-builder__slot:focus-visible .hw-rna-builder__slot-shape {\n stroke: var(--hw-accent);\n stroke-width: 2.5;\n}\n.hw-rna-builder__preview {\n margin: 6px 0;\n font-size: 11px;\n color: var(--hw-fg);\n font-family: ui-monospace, Menlo, Consolas, monospace;\n text-align: center;\n}\n.hw-rna-builder__add {\n display: block;\n width: 100%;\n padding: 4px 8px;\n background: var(--hw-accent);\n color: #ffffff;\n border: 1px solid var(--hw-accent);\n border-radius: 3px;\n font-size: 12px;\n font-weight: 600;\n cursor: pointer;\n}\n.hw-rna-builder__add:hover { opacity: 0.9; }\n.hw-rna-builder__add:active { transform: translateY(1px); }\n\n/* T-3513 -- RNA triplet chips. Small, monospace, wrap into a tight row.\n Used by the RNA pane\'s default-nucleotide row (r(A)p ... r(T)p) and by\n triplet favorites in the Favorites pane. Kept compact because the RNA\n pane\'s vertical space is constrained by the RNA builder above it. */\n.hw-triplet-chips {\n display: flex;\n flex-wrap: wrap;\n gap: 4px;\n padding: 2px;\n}\n.hw-triplet-chips--defaults {\n margin: 0 0 8px;\n}\n.hw-triplet-chip {\n position: relative;\n display: inline-flex;\n align-items: center;\n gap: 2px;\n height: 22px;\n padding: 0 6px;\n border: 1px solid var(--hw-border);\n border-radius: 11px;\n font-family: ui-monospace, Menlo, Consolas, monospace;\n font-size: 11px;\n font-weight: 600;\n line-height: 1;\n cursor: pointer;\n user-select: none;\n box-shadow: 0 1px 1px rgba(0, 0, 0, 0.08);\n transition: border-color 120ms, transform 120ms;\n}\n.hw-triplet-chip:hover {\n border-color: var(--hw-accent);\n transform: translateY(-1px);\n}\n.hw-triplet-chip--favorite { border-color: var(--hw-accent); }\n.hw-triplet-chip__star {\n font-size: 10px;\n cursor: pointer;\n color: var(--hw-muted);\n}\n.hw-triplet-chip--favorite .hw-triplet-chip__star { color: var(--hw-accent); }\n.hw-triplet-chip__label { letter-spacing: 0.02em; }\n\n/* Phase 29 (T-2901) -- The Phase 24 palette-level pick-mode hint\n container has been REMOVED. The hint now lives inside the RNA\n Builder as `.hw-rna-builder__hint` (see the rules under the RNA\n Builder block above). The user explicitly reported the\n reserved-space hint above the search box as "wasted space". */\n\n.hw-pane { display: block; }\n.hw-pane__content { font-family: ui-monospace, Menlo, Consolas, monospace; font-size: 12px; white-space: pre-wrap; word-break: break-all; }\n.hw-pane__notation {\n outline: none;\n border: 1px solid var(--hw-border);\n padding: 4px;\n background: var(--hw-bg);\n}\n.hw-pane__error { color: var(--hw-error); font-size: 11px; margin-top: 4px; display: none; }\n.hw-pane__error--visible { display: block; }\n.hw-pane__prop-row { display: flex; gap: 8px; padding: 2px 0; }\n.hw-pane__prop-label { color: var(--hw-muted); width: 180px; }\n.hw-pane__prop-value { color: var(--hw-fg); }\n.hw-pane__placeholder { color: var(--hw-muted); font-style: italic; }\n\n.hw-pane__content.hw-pane__sequence, .hw-pane__content.hw-pane__notation {\n max-height: 100px;\n overflow: scroll;\n}\n\n.hw-modal-backdrop {\n position: absolute;\n top: 0; left: 0; right: 0; bottom: 0;\n background: rgba(0,0,0,0.3);\n display: flex; align-items: center; justify-content: center;\n z-index: 1000;\n}\n.hw-modal {\n background: var(--hw-bg);\n color: var(--hw-fg);\n border: 1px solid var(--hw-border);\n border-radius: 4px;\n min-width: 320px;\n max-width: 600px;\n padding: 12px;\n}\n.hw-modal__header { font-weight: bold; padding-bottom: 8px; border-bottom: 1px solid var(--hw-border); }\n.hw-modal__body { padding-top: 8px; }\n.hw-modal__row { display: flex; gap: 8px; align-items: center; padding: 4px 0; }\n.hw-modal__label { color: var(--hw-fg); min-width: 100px; }\n.hw-modal__input, .hw-modal__select {\n flex: 1;\n padding: 4px;\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n background: var(--hw-bg);\n color: var(--hw-fg);\n}\n.hw-modal__check { transform: scale(1.1); }\n.hw-modal__actions { display: flex; justify-content: flex-end; gap: 6px; padding-top: 10px; }\n.hw-modal__ok, .hw-modal__cancel, .hw-modal__find-next, .hw-modal__replace, .hw-modal__replace-all {\n padding: 4px 10px;\n border: 1px solid var(--hw-border);\n background: var(--hw-bg);\n color: var(--hw-fg);\n border-radius: 3px;\n cursor: pointer;\n}\n.hw-modal__ok { background: var(--hw-accent); color: #ffffff; border-color: var(--hw-accent); }\n.hw-modal__result { color: var(--hw-muted); font-size: 11px; padding-top: 6px; }\n\n/* Phase 23 (T-2304) -- Bond editor endpoint preview row. Renders two\n monomer structures (atom A1 and atom A2) flanking a `↔` arrow so the\n user can see what they\'re connecting while picking R-groups. The\n SVG inside each cell stretches via the .hw-bond-props__atom-rdkit\n svg rule below (matches the tooltip pattern). */\n.hw-bond-props__atoms {\n display: flex;\n align-items: center;\n gap: 16px;\n margin: 12px 0;\n}\n.hw-bond-props__atom {\n flex: 1;\n text-align: center;\n}\n.hw-bond-props__atom-label {\n font-weight: 600;\n margin-bottom: 6px;\n color: var(--hw-fg);\n}\n.hw-bond-props__atom-rdkit {\n width: 180px;\n height: 120px;\n margin: 0 auto 8px;\n background: #fafafa;\n border: 1px solid #f3f4f6;\n border-radius: 4px;\n padding: 4px;\n box-sizing: border-box;\n}\n.hw-bond-props__atom-rdkit svg {\n display: block;\n width: 100%;\n height: 100%;\n}\n.hw-bond-props__bond-arrow {\n font-size: 24px;\n color: var(--hw-muted);\n flex: 0 0 auto;\n}\n\n.hw-editor-view {\n width: 100%;\n height: 100%;\n position: relative;\n --hw-hover: #ff8c00;\n}\n.hw-editor-view svg { width: 100%; height: 100%; }\n\n/* T-1103 / Phase 19 (T-1901) -- Cursor affordance only. We removed\n the :hover rules that recoloured the atom\'s own outline because\n they ran in PARALLEL with the real highlight ring painted by the\n renderer (teal #26A69A), producing the wrong colour the user\n reported as "yellow on hover" (the CSS rule re-stroked the atom in\n var(--hw-hover) = #ff8c00, an orange-yellow). The renderer\'s\n highlight layer is now the single source of truth for hover\n feedback. */\n.hw-atom { cursor: pointer; }\n.hw-bond { cursor: pointer; }\n\n/* Mode-specific cursors on the canvas wrapper. The editor adds an\n hw-editor-view--<mode> class via the option:change handler. */\n.hw-editor-view--select svg { cursor: default; }\n.hw-editor-view--eraser svg { cursor: not-allowed; }\n.hw-editor-view--hbond svg { cursor: crosshair; }\n.hw-editor-view--move svg { cursor: grab; }\n.hw-editor-view--move:active svg { cursor: grabbing; }\n\n/* Phase 22 (T-2201) -- Unified tooltip styling. Three tooltip variants\n share the same look-and-feel: atom hover (canvas), bond hover\n (canvas), palette-tile hover (left pane), and rna-builder slot hover.\n Pre-Phase 22 the tooltips were absolutely-positioned, dark, and\n z-index 100 -- the gallery panel (z-index higher) ate into them and\n the dark background looked heavy. Phase 22 mounts the tooltip at\n `document.body` (escaping every parent stacking context), pins\n `z-index: 99999`, and paints them white with a soft drop shadow and\n darker body text so they read clearly over any backdrop. */\n/* Phase 32 (T-3003) -- Ghost cursor preview that follows the mouse\n when a palette tile is primed in select mode. `pointer-events:\n none` so the underlying canvas keeps receiving clicks / drags. The\n z-index sits just below the tooltips (99998 vs 99999) so a real\n tooltip can still overlay the ghost if both happen to be visible. */\n.hw-next-add-cursor {\n position: fixed;\n pointer-events: none;\n z-index: 99998;\n opacity: 0.7;\n display: none;\n}\n.hw-next-add-cursor__svg {\n display: block;\n}\n\n.hw-atom-tooltip,\n.hw-bond-tooltip,\n.hw-palette-tooltip,\n.hw-builder-tooltip,\n.hw-toolbar-tooltip {\n position: fixed;\n pointer-events: none;\n background: #ffffff;\n color: #1f2937;\n border: 1px solid #e5e7eb;\n border-radius: 6px;\n box-shadow: 0 4px 16px rgba(0, 0, 0, 0.12), 0 2px 4px rgba(0, 0, 0, 0.08);\n padding: 10px 12px;\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 12px;\n line-height: 1.4;\n max-width: 240px;\n z-index: 99999;\n}\n/* T-3516 -- toolbar button tooltip: a single compact line, no wrap. */\n.hw-toolbar-tooltip {\n padding: 5px 8px;\n white-space: nowrap;\n font-weight: 500;\n}\n.hw-tooltip__symbol {\n font-weight: 700;\n color: #111827;\n}\n/* T-3514 -- RNA triplet tooltip: three monomer structures side by side.\n Wider than the single-structure tooltip so all three columns fit. */\n.hw-triplet-tooltip { max-width: 420px; }\n.hw-tooltip__triplet {\n display: flex;\n gap: 8px;\n margin-top: 6px;\n}\n.hw-tooltip__triplet-part {\n flex: 1 1 0;\n min-width: 0;\n text-align: center;\n}\n.hw-tooltip__triplet-role {\n font-weight: 600;\n color: #111827;\n font-size: 11px;\n}\n.hw-tooltip__name {\n color: #4b5563;\n}\n.hw-tooltip__hint {\n color: #6b7280;\n font-style: italic;\n font-size: 11px;\n margin-top: 6px;\n}\n.hw-tooltip__rdkit {\n display: block;\n margin-top: 8px;\n /* padding-top: 8px; */\n border-top: 1px solid #f3f4f6;\n background: #fafafa;\n border-radius: 4px;\n}\n/* Phase 23 (T-2303) -- The user reported "molecules do not take the full\n space" in the tooltip. RDKit emits an svg with a `viewBox`, so\n `width: 100%; height: auto` lets the structure stretch responsively\n to whatever width the parent tooltip column has. `max-height` caps\n tall structures so they never blow up the tooltip vertically. */\n.hw-tooltip__rdkit svg,\n[data-testid="atom-tooltip-rdkit-svg"] svg,\n[data-testid="palette-tooltip-rdkit-svg"] svg,\n[data-testid="builder-tooltip-rdkit-svg"] svg {\n display: block;\n width: 100%;\n height: auto;\n max-height: 180px;\n margin: 0 auto;\n}\n/* Legacy aliases (kept so Phase 21 atom-tooltip text styling still\n resolves). 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i?[i.get(t),t,o,4]:[this.undefinedColor,n,o,4]}return[this.undefinedColor,n,o,0]}}_.SemType="Aminoacids",_.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",_.undefinedColor="rgb(100,100,100)",_.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic 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Te={name:"dark",fallback:{line:"#e0e0e0",text:"#ffffff",background:ye("#eeeeee",.5)},errorTriple:{line:"#ff5050",text:"#ffffff",background:ye("#FFFF00",.4)},palette:{[Z]:Me(ve),[Q]:Me(we),[J]:Me(xe),[X]:Me(Ce),[ee]:Me(Ee),[te]:Me(ke),[ie]:Me(Be)}};function Ie(e,t,i=Se){if(null===e)return{...i.errorTriple};let n=e.meta?.colors;if(void 0!==n){let e="light"===i.name?n.light:"dark"===i.name?n.dark:void 0;if(void 0!==e)return{...e,line:Ae(e.background)};if(void 0!==n.default)return{...n.default,line:Ae(n.default.background)}}let o=e.naturalAnalog;if(void 0!==o&&""!==o){let e=i.palette[t];if(void 0!==e){let t=e[o];if(void 0!==t)return{...t,line:Ae(t.background),text:_e(t.background)}}}return{...i.fallback,line:Ae(i.fallback.background),text:_e(i.fallback.background)}}function Le(e){for(let t in e)if(Object.prototype.hasOwnProperty.call(e,t)&&"capgroupsmiles"===t.toLowerCase()){let i=e[t];if("string"==typeof i)return i}}function $e(e){switch(e.polymerType){case ne.PEPTIDE:return X;case ne.CHEM:return ee;case ne.BLOB:return te;case ne.RNA:if("Branch"===e.monomerType)return Z;if("Backbone"===e.monomerType){let t=e.naturalAnalog;return"P"===t||"p"===t?J:Q}return null;default:return null}}function Pe(e,t,i){return new Ne(e,t,i??{}).run()}new Set(["PEPTIDE","RNA","CHEM","BLOB"]),new Set(["Backbone","Branch","Terminal","Undefined"]);var Re=new Set(["?","*","_","X","N"]),He=/^R([1-9][0-9]*)$/,Ne=class{constructor(e,t,i){this.diagnostics=[],this.oldToNew=new Map,this.placeholderCache=new Map,this.mol=e,this.lib=t,this.options=i}run(){let e=new Map;for(let t of this.mol.chains)e.set(t.id,t.polymerType);for(let t of this.mol.atoms){let i=e.get(t.bio.chainId)??null,n=this.resolveAtom(t,i);this.oldToNew.set(t.id,n)}for(let e of this.mol.atoms){let t=this.oldToNew.get(e.id);if(void 0===t||void 0===e.branchAtom)continue;let i=this.oldToNew.get(e.branchAtom.id);void 0!==i&&(t.branchAtom=i)}let t=[];for(let e of this.mol.bonds){let i=this.oldToNew.get(e.a1.id),n=this.oldToNew.get(e.a2.id);void 0===i||void 0===n||t.push({...e,a1:i,a2:n})}let i=new Map;for(let e of t)i.set(e.id,e);let n=[];for(let e of this.mol.chains){let t=[];for(let i of e.backboneAtoms){let e=this.oldToNew.get(i.id);void 0!==e&&t.push(e)}let o=[];for(let t of e.bonds){let e=i.get(t.id);void 0!==e&&o.push(e)}n.push({id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:o,...void 0!==e.annotation?{annotation:e.annotation}:{},...void 0!==e.strandType?{strandType:e.strandType}:{}})}return{mol:{atoms:this.mol.atoms.map(e=>this.oldToNew.get(e.id)),bonds:t,chains:n,groups:this.mol.groups,annotations:this.mol.annotations},diagnostics:this.diagnostics}}resolveAtom(e,t){let i=null,n=e.biotype;if(null!==t){let o=this.lib.getMonomer(t,e.symbol);if(null!==o)i=this.toResolved(o),n=$e(o)??e.biotype;else if(this.isAmbiguitySymbol(e))i=this.synthesizeAmbiguity(t,e),this.emit("info","ambiguous-monomer",`Ambiguous monomer '${e.symbol}' on chain '${e.bio.chainId}'`,e);else if(se(e.symbol))i=this.registerInlineSmilesFallback(t,e);else if(!0===this.options.legacyCaseFallback&&"RNA"===t){let o=this.findCaseInsensitiveMatch(t,e.symbol);null!==o&&(i=this.toResolved(o),n=$e(o)??e.biotype,this.emit("info","case-mismatch",`Symbol '${e.symbol}' matched library entry '${o.symbol}' only after case fold`,e))}null===i&&(i=this.synthesizeMissing(t,e),this.emit("warning","unresolved-monomer",`Monomer '${e.symbol}' not found in library for ${t}`,e))}return{...e,monomer:i,biotype:n}}toResolved(e){let t=this.lib.getResolved?.(e);if(void 0!==t)return t;let i=new Map;for(let t of e.rgroups){let e=He.exec(t.label);null!==e&&i.set(parseInt(e[1],10),t)}return Object.assign({},e,{rs:e.rgroups.length,rgroupMap:i})}isAmbiguitySymbol(e){return!(!Re.has(e.symbol)&&void 0===e.bio.ambiguity)}synthesizeAmbiguity(e,t){let i=`ambig:${e}:${t.symbol}`,n=this.placeholderCache.get(i);return void 0===n&&(n={symbol:t.symbol,polymerType:e,monomerType:"Undefined",molfile:"",rgroups:[{label:"R1",capGroupName:"H",capGroupSMILES:""},{label:"R2",capGroupName:"H",capGroupSMILES:""}],meta:{ambiguous:!0}},this.placeholderCache.set(i,n)),this.toResolved(n)}synthesizeMissing(e,t){let i=`missing:${e}:${t.symbol}`,n=this.placeholderCache.get(i);return void 0===n&&(n={symbol:t.symbol,polymerType:e,monomerType:"Undefined",molfile:"",rgroups:[{label:"R1",capGroupName:"H",capGroupSMILES:""},{label:"R2",capGroupName:"H",capGroupSMILES:""}],meta:{missing:!0}},this.placeholderCache.set(i,n)),this.toResolved(n)}registerInlineSmilesFallback(e,t){if("function"==typeof this.lib.registerInlineSmilesMonomer)try{let i=this.lib.registerInlineSmilesMonomer(e,t.symbol);return this.toResolved(i)}catch{this.emit("warning","inline-smiles-without-r-groups",`Inline SMILES '${i=t.symbol,i.length<=40?i:i.slice(0,39)+"…"}' has no detectable R-groups`,t)}else this.emit("warning","inline-smiles-without-r-groups","Inline SMILES seen but lib has no registerInlineSmilesMonomer",t);var i;return this.synthesizeMissing(e,t)}findCaseInsensitiveMatch(e,t){let i=t.toLowerCase();for(let n of this.lib.getMonomerSymbolsByType(e))if(n.toLowerCase()===i&&n!==t){let t=this.lib.getMonomer(e,n);if(null!==t)return t}return null}emit(e,t,i,n){let o={chainId:n.bio.chainId,atomId:n.id,symbol:n.symbol};this.diagnostics.push({severity:e,code:t,message:i,context:o})}};function De(e,t,i){let n,o=i?.mode??"lenient";try{n=function(e){let t=new q(e).tokenize();return function(e){let t=null;for(let i of e.tokens)if("apos"===i.kind)t=null===t?i.span:null;else if("eof"===i.kind&&null!==t)throw new R("unterminated-apostrophe",`Unterminated apostrophe block starting at offset ${t.start}`,{span:{start:t.start,end:e.source.length}})}(t),t}(e)}catch(e){if(e instanceof R){if("strict"===o)throw e;let t={severity:"error",code:e.code,message:e.message,...void 0!==e.span?{span:{start:e.span.start,end:e.span.end}}:{}};return{mol:Y(),diagnostics:[t]}}throw e}return function(e,t,i){let n=new Ge(e,t,i?.mode??"lenient").parseDocument();if(null===t||!1===i?.resolveMonomers)return n;let o=Pe(n.mol,t,{mode:i?.mode??"lenient",...!0===i?.legacyCaseFallback?{legacyCaseFallback:!0}:{}});return{mol:o.mol,diagnostics:[...n.diagnostics,...o.diagnostics]}}(n,t,i)}var Fe=class{constructor(e){this.tokens=e.tokens,this.len=e.tokens.length,this.eof=e.tokens[e.tokens.length-1],this.idx=0}peek(e=0){let t=this.idx+e;return t>=this.len?this.eof:this.tokens[t]}advance(){let e=this.idx<this.len?this.tokens[this.idx]:this.eof;return"eof"!==e.kind&&(this.idx+=1),e}optional(e){let t=this.idx<this.len?this.tokens[this.idx]:this.eof;return t.kind===e?("eof"!==t.kind&&(this.idx+=1),t):null}at(e){return(this.idx<this.len?this.tokens[this.idx]:this.eof).kind===e}at2(e,t){let i=(this.idx<this.len?this.tokens[this.idx]:this.eof).kind;return i===e||i===t}at3(e,t,i){let n=(this.idx<this.len?this.tokens[this.idx]:this.eof).kind;return n===e||n===t||n===i}currentSpan(){return(this.idx<this.len?this.tokens[this.idx]:this.eof).span}position(){return this.idx}setPosition(e){this.idx=e}isAtEnd(){return"eof"===(this.idx<this.len?this.tokens[this.idx]:this.eof).kind}},Oe=/^(PEPTIDE|RNA|DNA|CHEM|BLOB|G)([0-9]+)$/;function ze(e){let t=Oe.exec(e);if(null===t)return null;let i=t[1],n=parseInt(t[2],10);switch(i){case"PEPTIDE":return{rawTypeName:"PEPTIDE",polymerType:ne.PEPTIDE,number:n,isDnaShim:!1,isGroup:!1};case"RNA":return{rawTypeName:"RNA",polymerType:ne.RNA,number:n,isDnaShim:!1,isGroup:!1};case"DNA":return{rawTypeName:"DNA",polymerType:ne.RNA,number:n,isDnaShim:!0,isGroup:!1};case"CHEM":return{rawTypeName:"CHEM",polymerType:ne.CHEM,number:n,isDnaShim:!1,isGroup:!1};case"BLOB":return{rawTypeName:"BLOB",polymerType:ne.BLOB,number:n,isDnaShim:!1,isGroup:!1};case"G":return{rawTypeName:"G",polymerType:ne.PEPTIDE,number:n,isDnaShim:!1,isGroup:!0};default:return null}}var Ge=class{constructor(e,t,i){this.diagnostics=[],this.chains=[],this.chainById=new Map,this.pendingBonds=[],this.groups=[],this.atomIds=new oe,this.bondIds=new oe,this.cursor=new Fe(e),this.source=e.source,this.lib=t,this.mode=i,this.annotations={perPolymer:new Map,version:""}}parseDocument(){if(this.cursor.isAtEnd())return this.emit("warning","empty-helm","Empty HELM string"),{mol:Y(),diagnostics:this.diagnostics};if(this.parseSimplePolymers(),this.expectDollarSeparator(1),this.parseConnections(),this.expectDollarSeparator(2),this.parseGroupsSection(),this.expectDollarSeparator(3),this.parseAnnotationsSection(),this.cursor.at("dollar")&&(this.cursor.advance(),this.parseVersionTrailer()),!this.cursor.isAtEnd())for(this.emit("warning","extra-section-separator","Unexpected trailing tokens after HELM document",this.cursor.currentSpan());!this.cursor.isAtEnd();)this.cursor.advance();return{mol:this.finalize(),diagnostics:this.diagnostics}}expectDollarSeparator(e){this.cursor.at("dollar")?this.cursor.advance():this.emit("error","missing-section-separator",`Expected '$' separator before section ${e+1}`,this.cursor.currentSpan())}parseSimplePolymers(){if(!this.cursor.at("dollar")&&!this.cursor.isAtEnd())for(this.parsePolymer();this.cursor.at("pipe");){if(this.cursor.advance(),this.cursor.at("dollar")||this.cursor.isAtEnd())return void this.emit("warning","empty-polymer-body","Empty polymer after '|'",this.cursor.currentSpan());this.parsePolymer()}}parsePolymer(){let e=this.cursor.currentSpan(),t=this.cursor.optional("identifier");if(null===t)return this.emit("error","unexpected-token",`Expected polymer id, got '${this.cursor.peek().value}'`,this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let i=ze(t.value);if(null===i)return this.emit("error","unknown-polymer-type",`Unknown polymer type '${t.value}'`,t.span),void this.skipUntil(["pipe","dollar","eof"]);if(this.chainById.has(t.value)&&this.emit("warning","duplicate-polymer-id",`Duplicate polymer id '${t.value}'`,t.span),null===this.cursor.optional("lbrace"))return void this.emit("error","unexpected-token",`Expected '{' after polymer id '${t.value}'`,this.cursor.currentSpan());let n={id:t.value,polymerType:i.polymerType,rawTypeName:i.rawTypeName,rawNumber:i.number,backboneAtoms:[],allAtoms:[],bonds:[],span:{start:e.start,end:e.end}};if(this.chains.push(n),this.chainById.set(n.id,n),this.cursor.at("rbrace"))this.emit("warning","empty-polymer-body",`Empty body for polymer '${n.id}'`,this.cursor.currentSpan());else if(i.isGroup)this.parseGroupBody(n);else switch(i.polymerType){case ne.PEPTIDE:this.parsePeptideBody(n);break;case ne.RNA:this.parseRnaBody(n,i.isDnaShim),i.isDnaShim&&this.emit("info","dna-emitted-as-rna",`DNA polymer '${n.id}' will be emitted as RNA on canonicalize`,t.span);break;case ne.CHEM:this.parseChemBody(n);break;case ne.BLOB:this.parseBlobBody(n)}if(null===this.cursor.optional("rbrace"))return this.emit("error","unterminated-brace",`Expected '}' to close polymer '${n.id}'`,this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let o=this.cursor.optional("quote-string");null!==o&&(n.annotation=o.value)}parsePeptideBody(e){for(this.parsePeptideItem(e);this.cursor.at("dot")&&(this.cursor.advance(),!this.cursor.at("rbrace")&&!this.cursor.at("gt"));)this.parsePeptideItem(e);if(this.cursor.at("gt")){let t=this.cursor.currentSpan();this.cursor.advance(),this.emit("warning","peptide-cyclic-without-closure",`Peptide '${e.id}' marked cyclic with '>' — no explicit closure connection emitted`,t)}}parsePeptideItem(e){if(this.cursor.at("lparen"))this.parsePeptideAlternation(e);else{let t=this.parsePeptideAtom(e);this.maybeRepeatBracket(e,[t])}this.maybeAttachAnnotation(e)}parsePeptideAtom(e){let t=this.consumeMonomerSymbol(!1),{symbol:i,annotation:n,ambiguity:o,ambiguityKind:r,isInlineSmiles:s,rawPayload:a,inlineSource:l,span:h}=t,d=this.makeAtom(e,X,i);void 0!==n&&(d.tag=n),void 0!==o&&(d.bio.ambiguity=o),void 0!==r&&(d.bio.ambiguityKind=r),void 0!==l&&(d.inlineSource=l),s&&this.registerInlineSmiles(a,h,ne.PEPTIDE),this.addToChain(e,d,!0);let c=e.backboneAtoms[e.backboneAtoms.length-2];return void 0!==c&&this.addBond(e,c,d,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1}),d}parsePeptideAlternation(e){let t=this.cursor.currentSpan();if(this.cursor.advance(),this.peptideContentIsSubsequence()){let t=e.backboneAtoms.length;for(this.parsePeptideItem(e);this.cursor.at("dot")&&(this.cursor.advance(),!this.cursor.at("rparen")&&!this.cursor.isAtEnd());)this.parsePeptideItem(e);null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' to close repeat sub-sequence",this.cursor.currentSpan());let i=e.backboneAtoms.slice(t);return this.maybeRepeatBracket(e,i),void this.maybeAttachAnnotation(e)}let i=[],n=null;for(;!this.cursor.at("rparen")&&!this.cursor.isAtEnd();){let e=this.parseAlternationCandidate(ne.PEPTIDE);if(i.push(e),this.cursor.at("comma"))"and"===n&&this.emit("warning","mixed-separator-in-alternation","Mixed ',' and '+' separators in alternation",this.cursor.currentSpan()),n="or",this.cursor.advance();else{if(!this.cursor.at("plus"))break;"or"===n&&this.emit("warning","mixed-separator-in-alternation","Mixed ',' and '+' separators in alternation",this.cursor.currentSpan()),n="and",this.cursor.advance()}}null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' to close alternation",this.cursor.currentSpan());let o="and"===n?"+":",",r=`(${i.map(e=>e.symbol+(void 0!==e.ratio?`:${String(e.ratio)}`:"")).join(o)})`,s=this.makeAtom(e,X,"?");s.bio.ambiguity=r,s.bio.ambiguityKind="and"===n?"and":"or",this.addToChain(e,s,!0);let a=e.backboneAtoms[e.backboneAtoms.length-2];if(void 0!==a&&this.addBond(e,a,s,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1}),"and"===n)for(let e of i)"number"==typeof e.ratio&&e.ratio<0&&this.emit("error","ratio-and-negative",`Negative ratio ${e.ratio} in AND mixture`,t);this.maybeRepeatBracket(e,[s]),this.maybeAttachAnnotation(e)}peptideContentIsSubsequence(){let e=1,t=0;for(;;){let i=this.cursor.peek(t);if("eof"===i.kind)return!1;if("lparen"!==i.kind)if("rparen"!==i.kind){if(1===e){if("dot"===i.kind)return!0;if("comma"===i.kind||"plus"===i.kind||"colon"===i.kind)return!1}if(t+=1,t>1024)return!1}else{if(e-=1,0===e)return!0;t+=1}else e+=1,t+=1}}parseAlternationCandidate(e){let t,{symbol:i,isInlineSmiles:n,rawPayload:o,span:r}=this.consumeMonomerSymbol(!0);if(n&&this.registerInlineSmiles(o,r,e),null!==this.cursor.optional("colon")){let e=this.cursor.peek();"integer"===e.kind||"decimal"===e.kind?(this.cursor.advance(),t=parseFloat(e.value)):"question"===e.kind?(this.cursor.advance(),t="?"):this.emit("error","unexpected-token","Expected ratio after ':' in alternation",e.span)}return void 0===t?{symbol:i}:{symbol:i,ratio:t}}parseRnaBody(e,t){for(this.parseRnaItem(e,t);this.cursor.at("dot")&&(this.cursor.advance(),!(this.cursor.at("rbrace")||this.cursor.at("dollar")||this.cursor.isAtEnd()));)this.parseRnaItem(e,t)}parseRnaItem(e,t){if(this.cursor.at("lparen"))return void this.parseRnaAlternation(e,t);if(this.cursor.at("asterisk")){this.cursor.currentSpan(),this.cursor.advance();let t=this.makeAtom(e,ie,"*");this.addToChain(e,t,!0);let i=e.backboneAtoms[e.backboneAtoms.length-2];return void 0!==i&&this.addBond(e,i,t,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1}),this.maybeRepeatBracket(e,[t]),void this.maybeAttachAnnotation(e)}let i,n,o=this.parseRnaSugar(e,t);this.maybeAttachAnnotation(e),this.cursor.at("lparen")&&(this.cursor.advance(),this.cursor.at("rparen")||(i=this.parseRnaBaseSymbol(e),this.maybeAttachAnnotationTo(i)),null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' after RNA base",this.cursor.currentSpan()),void 0!==i&&(this.addBond(e,o,i,"branch",{kind:"numeric",r:3},{kind:"numeric",r:1}),o.branchAtom=i)),this.canStartRnaLinker()&&(n=this.parseRnaLinker(e),this.maybeAttachAnnotationTo(n)),void 0!==n&&this.addBond(e,o,n,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1});let r=e.backboneAtoms.indexOf(o);if(r>0){let t=e.backboneAtoms[r-1];this.addBond(e,t,o,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1})}let s=[o];void 0!==i&&s.push(i),void 0!==n&&s.push(n),this.maybeRepeatBracket(e,s)}canStartRnaLinker(){let e=this.cursor.peek().kind;return"identifier"===e||"inline-smiles"===e||"asterisk"===e}parseRnaSugar(e,t){let{symbol:i,isInlineSmiles:n,rawPayload:o,inlineSource:r,span:s}=this.consumeMonomerSymbol(!1),a=this.makeAtom(e,Q,i);return void 0!==r&&(a.inlineSource=r),n&&this.registerInlineSmiles(o,s,ne.RNA),this.addToChain(e,a,!0),a}parseRnaBaseSymbol(e){let{symbol:t,isInlineSmiles:i,rawPayload:n,inlineSource:o,span:r}=this.consumeMonomerSymbol(!1),s=this.makeAtom(e,Z,t);return void 0!==o&&(s.inlineSource=o),i&&this.registerInlineSmiles(n,r,ne.RNA),this.addToChain(e,s,!1),s}parseRnaLinker(e){if(this.cursor.at("asterisk")){this.cursor.currentSpan(),this.cursor.advance();let t=this.makeAtom(e,J,"*");return this.addToChain(e,t,!0),t}let{symbol:t,isInlineSmiles:i,rawPayload:n,inlineSource:o,span:r}=this.consumeMonomerSymbol(!1),s=this.makeAtom(e,J,t);return void 0!==o&&(s.inlineSource=o),i&&this.registerInlineSmiles(n,r,ne.RNA),this.addToChain(e,s,!0),s}parseRnaAlternation(e,t){let i=e.backboneAtoms.length;if(this.cursor.advance(),this.looksLikeFlatAlternation()){let t=[],i=null;for(;!this.cursor.at("rparen")&&!this.cursor.isAtEnd();)if(t.push(this.parseAlternationCandidate(ne.RNA)),this.cursor.at("comma"))i="or",this.cursor.advance();else{if(!this.cursor.at("plus"))break;i="and",this.cursor.advance()}null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' in RNA alternation",this.cursor.currentSpan());let n="and"===i?"+":",",o=`(${t.map(e=>e.symbol+(void 0!==e.ratio?`:${String(e.ratio)}`:"")).join(n)})`,r=this.makeAtom(e,Z,"?");r.bio.ambiguity=o,r.bio.ambiguityKind="and"===i?"and":"or",this.addToChain(e,r,!0);let s=e.backboneAtoms[e.backboneAtoms.length-2];return void 0!==s&&this.addBond(e,s,r,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1}),this.maybeRepeatBracket(e,[r]),void this.maybeAttachAnnotation(e)}for(this.parseRnaItem(e,t);this.cursor.at("dot")&&(this.cursor.advance(),!this.cursor.at("rparen")&&!this.cursor.isAtEnd());)this.parseRnaItem(e,t);null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' in RNA repeat",this.cursor.currentSpan());let n=e.backboneAtoms.slice(i);this.maybeRepeatBracket(e,n),this.maybeAttachAnnotation(e)}looksLikeFlatAlternation(){let e=1,t=0,i=!1;for(;;){let n=this.cursor.peek(t);if("eof"===n.kind)return i;if("rparen"===n.kind){if(e-=1,0===e)return i}else{if("lparen"===n.kind)return!1;if("dot"===n.kind)return!1;1===e&&("comma"===n.kind||"plus"===n.kind)&&(i=!0)}if(t+=1,t>256)return i}}parseChemBody(e){let t;if(this.cursor.at("asterisk"))this.cursor.advance(),t=this.makeAtom(e,ee,"*"),this.addToChain(e,t,!0);else{let{symbol:i,isInlineSmiles:n,rawPayload:o,inlineSource:r,span:s}=this.consumeMonomerSymbol(!1);t=this.makeAtom(e,ee,i),void 0!==r&&(t.inlineSource=r),n&&this.registerInlineSmiles(o,s,ne.CHEM),this.addToChain(e,t,!0)}this.maybeAttachAnnotation(e),this.cursor.at("apos")&&this.maybeRepeatBracket(e,[t]),this.cursor.at("rbrace")||(this.emit("error","chem-multiple-monomers",`CHEM polymer '${e.id}' must contain exactly one monomer`,this.cursor.currentSpan()),this.skipUntil(["rbrace","eof"]))}parseBlobBody(e){let t,i,n,o=!1,r="",s=this.cursor.currentSpan();if(this.cursor.at("inline-smiles")){let e=this.cursor.advance();o=se(e.value),r=e.value,t=e.value,i=e.value,n=e.value,s=e.span}else if(this.cursor.at("identifier")){let e=this.cursor.advance();t=e.value,i=e.value,s=e.span}else this.emit("error","unknown-blobtype","Expected BLOB identifier",this.cursor.currentSpan()),t="?",i="?";let a=this.makeAtom(e,te,t);a.bio.blobtype=i,void 0!==n&&(a.inlineSource=n),o&&this.registerInlineSmiles(r,s,ne.BLOB),this.addToChain(e,a,!0),this.maybeAttachAnnotation(e)}parseGroupBody(e){let t=0;for(;;){let e=this.cursor.peek();if("eof"===e.kind||0===t&&"rbrace"===e.kind)break;"lbrace"===e.kind&&(t+=1),"rbrace"===e.kind&&(t-=1),this.cursor.advance()}}parseConnections(){if(!this.cursor.at("dollar")&&!this.cursor.isAtEnd())for(this.parseConnection();this.cursor.at("pipe")&&(this.cursor.advance(),!this.cursor.at("dollar")&&!this.cursor.isAtEnd());)this.parseConnection()}parseConnection(){let e=this.cursor.currentSpan(),t=this.cursor.optional("identifier");if(null===t)return this.emit("error","unexpected-token","Expected chain id in connection",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);if(null===this.cursor.optional("comma"))return this.emit("error","unexpected-token","Expected ',' in connection",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let i=this.cursor.optional("identifier");if(null===i)return this.emit("error","unexpected-token","Expected second chain id in connection",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);if(null===this.cursor.optional("comma"))return this.emit("error","unexpected-token","Expected ',' before connection position",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let n=this.parsePosition();if(null===this.cursor.optional("colon"))return this.emit("error","unexpected-token","Expected ':' between position and R-group",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let o=this.parseRGroupSpec();if(null===this.cursor.optional("dash"))return this.emit("error","unexpected-token","Expected '-' between connection endpoints",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let r=this.parsePosition();if(null===this.cursor.optional("colon"))return this.emit("error","unexpected-token","Expected ':' before second R-group",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let s=this.parseRGroupSpec(),a=this.cursor.optional("quote-string"),l="pair"===o.kind&&"pair"===s.kind?"hbond":"cross-polymer",h={chain1:t.value,pos1:n,r1:o,chain2:i.value,pos2:r,r2:s,kind:l,span:{start:e.start,end:a?.span.end??this.cursor.peek().span.start},...null!==a?{tag:a.value}:{}};this.pendingBonds.push(h)}parsePosition(){let e=this.cursor.peek();return"integer"===e.kind?(this.cursor.advance(),{kind:"index",value:parseInt(e.value,10)}):"question"===e.kind?(this.cursor.advance(),{kind:"any"}):"identifier"===e.kind?(this.cursor.advance(),this.emit("info","symbol-position-reference",`Connection position uses monomer symbol '${e.value}' as chain-level ambiguity`,e.span),{kind:"symbol",value:e.value}):(this.emit("error","invalid-position",`Expected position (integer, '?', or symbol), got '${e.value}'`,e.span),{kind:"any"})}parseRGroupSpec(){let e=this.cursor.peek();if("question"===e.kind)return this.cursor.advance(),{kind:"unspecified"};if("asterisk"===e.kind)return this.cursor.advance(),{kind:"wildcard"};if("identifier"===e.kind){if(this.cursor.advance(),"pair"===e.value)return{kind:"pair"};let t=/^R([1-9][0-9]*)$/.exec(e.value);return null===t?(this.emit("error","invalid-rgroup",`Expected R-group label, got '${e.value}'`,e.span),{kind:"unspecified"}):{kind:"numeric",r:parseInt(t[1],10)}}return this.emit("error","invalid-rgroup",`Expected R-group label, got '${e.value}'`,e.span),{kind:"unspecified"}}parseGroupsSection(){if(!this.cursor.at("dollar")&&!this.cursor.isAtEnd())for(this.parseGroupOrBondRatio();this.cursor.at("pipe")&&(this.cursor.advance(),!this.cursor.at("dollar")&&!this.cursor.isAtEnd());)this.parseGroupOrBondRatio()}parseGroupOrBondRatio(){let e=this.cursor.optional("identifier");if(null===e)return this.emit("error","unexpected-token","Expected group or bond-ratio identifier",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);this.cursor.at("lparen")?this.parseGroupAfterId(e):this.cursor.at("plus")?this.parseBondRatioAfterId(e):(this.emit("warning","unexpected-token",`Expected '(' or '+' after id '${e.value}' in section 3`,this.cursor.currentSpan()),this.skipUntil(["pipe","dollar","eof"]))}parseGroupAfterId(e){let t=ze(e.value);(null===t||!t.isGroup)&&this.emit("error","unknown-group-reference",`Group id must be 'G<n>', got '${e.value}'`,e.span),this.cursor.advance();let i=[],n="or",o=null;for(;!this.cursor.at("rparen")&&!this.cursor.isAtEnd();){let e=this.parseGroupMember();if(null!==e&&i.push(e),this.cursor.at("comma"))null===o&&(o="or",n="or"),this.cursor.advance();else{if(!this.cursor.at("plus"))break;null===o&&(o="and",n="and"),this.cursor.advance()}}null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' to close group",this.cursor.currentSpan()),this.groups.push({id:e.value,kind:n,members:i})}parseGroupMember(){let e,t=this.cursor.optional("identifier");return null===t?(this.emit("error","unexpected-token","Expected group member id",this.cursor.currentSpan()),null):(null!==this.cursor.optional("colon")&&(e=this.parseRatio()),void 0===e?{target:t.value}:{target:t.value,ratio:e})}parseRatio(){let e=this.cursor.peek();if("integer"===e.kind||"decimal"===e.kind){this.cursor.advance();let t=parseFloat(e.value);if(this.cursor.at("dash")&&(this.cursor.peek(),"integer"===this.cursor.peek(1).kind)){this.cursor.advance();let t=this.cursor.advance();this.emit("info","ratio-range",`Ratio range ${e.value}-${t.value}; using lower bound`,{start:e.span.start,end:t.span.end})}return t}return"question"===e.kind?(this.cursor.advance(),"?"):(this.emit("error","unexpected-token",`Expected ratio after ':', got '${e.value}'`,e.span),0)}parseBondRatioAfterId(e){this.cursor.advance();let t,i=this.cursor.optional("identifier");if(null===i)return void this.emit("error","unexpected-token","Expected second chain id in bond-ratio",this.cursor.currentSpan());if(null!==this.cursor.optional("colon")){let e=this.parseRatio();"number"==typeof e&&(t=e)}let n=this.pendingBonds.find(t=>t.chain1===e.value&&t.chain2===i.value||t.chain1===i.value&&t.chain2===e.value);void 0!==n?void 0!==t&&(n.ratio={numerator:t}):this.emit("warning","bond-ratio-no-matching-bond",`Bond-ratio for ${e.value}+${i.value} has no matching cross-polymer bond`,e.span)}parseAnnotationsSection(){if(!this.cursor.at("dollar")&&!this.cursor.isAtEnd()){if(this.cursor.position(),this.cursor.at("lbrace"))return this.parseAnnotation20(),void(this.cursor.at("pipe")&&(this.emit("info","annotation-mixed-versions","Mixed HELM 2.0 JSON and HELM 1.0 pipe annotations",this.cursor.currentSpan()),this.cursor.advance(),this.parseAnnotation10Entries()));this.parseAnnotation10Entries()}}parseAnnotation20(){let e=this.cursor.currentSpan(),t=0,i=e.end;for(;!this.cursor.isAtEnd();){let e=this.cursor.peek();if("lbrace"===e.kind)t+=1;else if("rbrace"===e.kind&&(t-=1,0===t)){i=e.span.end,this.cursor.advance();break}this.cursor.advance()}let n=this.source.slice(e.start,i),o=null;try{o=JSON.parse(n)}catch{return this.emit("warning","annotation-malformed-json","Annotation block is not valid JSON",{start:e.start,end:i}),void(this.annotations={perPolymer:this.annotations.perPolymer,version:this.annotations.version,raw:n})}if(null===o||"object"!=typeof o||Array.isArray(o))this.emit("warning","annotation-malformed-json","Annotation block parsed but is not an object",{start:e.start,end:i}),this.annotations={perPolymer:this.annotations.perPolymer,version:this.annotations.version,raw:n};else{let t=new Map(this.annotations.perPolymer);for(let[i,n]of Object.entries(o))null===n||"object"!=typeof n||Array.isArray(n)?t.set(i,{value:n}):(t.set(i,{...n}),this.chainById.has(i)||this.emit("warning","annotation-unknown-polymer",`Annotation references unknown polymer '${i}'`,e));this.annotations={perPolymer:t,version:this.annotations.version}}}parseAnnotation10Entries(){for(this.parseAnnotation10One();this.cursor.at("pipe")&&(this.cursor.advance(),!this.cursor.at("dollar")&&!this.cursor.isAtEnd());)this.parseAnnotation10One()}parseAnnotation10One(){let e=this.cursor.optional("identifier");if(null===e)return this.emit("warning","annotation-malformed-json","Expected polymer-id in HELM 1.0 annotation",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);if(null===this.cursor.optional("lbrace"))return this.emit("warning","annotation-malformed-json","Expected '{' after polymer-id",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let t=[];for(;!this.cursor.at("rbrace")&&!this.cursor.isAtEnd();)t.push(this.cursor.advance().value);if(null===this.cursor.optional("rbrace"))return void this.emit("error","unterminated-brace","Expected '}' to close annotation",this.cursor.currentSpan());let i=t.join("").trim(),n=new Map(this.annotations.perPolymer),o=n.get(e.value)??{};"ss"===i||"as"===i?n.set(e.value,{...o,strandtype:i}):n.set(e.value,{...o,[i]:!0}),this.chainById.has(e.value)||this.emit("warning","annotation-unknown-polymer",`Annotation references unknown polymer '${e.value}'`,e.span),this.annotations={perPolymer:n,version:this.annotations.version}}parseVersionTrailer(){let e=this.cursor.optional("identifier");if(null===e)return void(this.annotations={...this.annotations,version:""});let t=e.value;if(this.cursor.at("dot")&&"integer"===this.cursor.peek(1).kind){this.cursor.advance();let i=this.cursor.advance();t=`${e.value}.${i.value}`}this.annotations={...this.annotations,version:t}}skipUntil(e){for(;!this.cursor.isAtEnd();){if(e.includes(this.cursor.peek().kind))return;this.cursor.advance()}}consumeMonomerSymbol(e){let t=this.cursor.peek();if("inline-smiles"===t.kind){this.cursor.advance();let e=se(t.value);return{symbol:t.value,isInlineSmiles:e,rawPayload:t.value,inlineSource:t.value,span:t.span}}if("identifier"===t.kind){this.cursor.advance();let e=t.value,i=t.span;for(;"dash"===this.cursor.peek().kind&&"integer"===this.cursor.peek(1).kind&&("identifier"===this.cursor.peek(2).kind||"dash"===this.cursor.peek(2).kind);){this.cursor.advance();let t=this.cursor.advance();if(e=`${e}-${t.value}`,i=t.span,"identifier"===this.cursor.peek().kind){let t=this.cursor.advance();e=`${e}${t.value}`,i=t.span}}return{symbol:e,isInlineSmiles:!1,rawPayload:e,span:{start:t.span.start,end:i.end}}}if("asterisk"===t.kind||"underscore"===t.kind||"question"===t.kind)return this.cursor.advance(),{symbol:t.value,isInlineSmiles:!1,rawPayload:t.value,span:t.span};if("integer"===t.kind&&"identifier"===this.cursor.peek(1).kind){let e=this.cursor.advance(),t=this.cursor.advance(),i=`${e.value}${t.value}`;return{symbol:i,isInlineSmiles:!1,rawPayload:i,span:{start:e.span.start,end:t.span.end}}}return this.emit("error","unexpected-token",`Expected monomer symbol, got '${t.value}'`,t.span),{symbol:"?",isInlineSmiles:!1,rawPayload:"",span:t.span}}maybeRepeatBracket(e,t){if(!this.cursor.at("apos"))return;let i=this.cursor.currentSpan();this.cursor.advance();let n=this.cursor.optional("integer");if(null===n)return this.emit("error","unexpected-token","Expected integer in repeat bracket",this.cursor.currentSpan()),void this.cursor.optional("apos");let o=parseInt(n.value,10),r=o;if(this.cursor.at("dash")){this.cursor.advance();let e=this.cursor.optional("integer");null===e?this.emit("error","unexpected-token","Expected integer after '-' in repeat bracket",this.cursor.currentSpan()):r=parseInt(e.value,10)}if(null===this.cursor.optional("apos")&&this.emit("error","unterminated-apostrophe","Expected closing apostrophe",this.cursor.currentSpan()),0!==t.length){if(r<o){this.emit("warning","repeat-range-inverted",`Repeat range ${o}-${r} has max < min; swapping`,i);let e=o;o=r,r=e}0!==o||0!==r?(r>1e4&&this.emit("warning","bracket-repeat-too-large",`Repeat range upper bound ${r} > 10000`,i),e.polymerType===ne.CHEM&&this.emit("error","repeat-on-non-iterable-polymer",`Repeat bracket not allowed on CHEM polymer '${e.id}'`,i),this.groups.push({id:`${e.id}/bracket@${t[0]?.id??0}`,kind:"bracket",members:t.map(e=>({target:String(e.id)})),repeat:{min:o,max:r}})):this.emit("warning","repeat-zero-count","Repeat bracket with zero count",i)}else this.emit("warning","repeat-on-empty-bracket","Repeat bracket applied to empty content",i)}maybeAttachAnnotation(e){let t=e.backboneAtoms[e.backboneAtoms.length-1];void 0!==t&&this.maybeAttachAnnotationTo(t)}maybeAttachAnnotationTo(e){if(void 0===e)return;let t=this.cursor.optional("quote-string");null!==t&&(e.tag=t.value)}registerInlineSmiles(e,t,i){if(se(e)){if(null===this.lib)return void this.emit("info","inline-smiles-no-lib","Inline SMILES seen but no monomer library available for registration",t);try{this.lib.addMonomer;let t=this.lib.registerInlineSmilesMonomer;"function"==typeof t&&t.call(this.lib,i,e)}catch(e){let i=e instanceof Error?e.message:String(e);this.emit("warning","inline-smiles-without-r-groups",`Inline SMILES registration failed: ${i}`,t)}}}makeAtom(e,t,i){return{id:this.atomIds.next(),p:{x:0,y:0},biotype:t,symbol:i,monomer:null,bio:{chainId:e.id,positionInChain:0,continuousId:0},hidden:!1,selected:!1,highlighted:!1}}addToChain(e,t,i){e.allAtoms.push(t),i&&(e.backboneAtoms.push(t),t.bio.positionInChain=e.backboneAtoms.length)}addBond(e,t,i,n,o,r){let s=this.bondIds.next();e.bonds.push({id:s,a1:t,a2:i,kind:n,r1:o,r2:r})}finalize(){let e=[];for(let t of this.pendingBonds){let i=this.chainById.get(t.chain1),n=this.chainById.get(t.chain2);if(void 0===i){this.emit("error","unknown-chain-reference",`Connection references unknown chain '${t.chain1}'`,t.span);continue}if(void 0===n){this.emit("error","unknown-chain-reference",`Connection references unknown chain '${t.chain2}'`,t.span);continue}let o=this.resolveAtomByPosition(i,t.pos1,t.span),r=this.resolveAtomByPosition(n,t.pos2,t.span);if(null===o||null===r)continue;"pair"===t.r1.kind&&void 0!==o.branchAtom&&(o=o.branchAtom),"pair"===t.r2.kind&&void 0!==r.branchAtom&&(r=r.branchAtom);let s={id:this.bondIds.next(),a1:o,a2:r,kind:t.kind,r1:t.r1,r2:t.r2,...void 0!==t.tag?{tag:t.tag}:{},...void 0!==t.ratio?{ratio:t.ratio}:{}};e.push(s)}let t=[],i=[],n=[];for(let e of this.chains){for(let i of e.allAtoms)t.push(i);for(let t of e.bonds)i.push(t);let o=this.annotations.perPolymer.get(e.id),r=void 0===o?void 0:o.strandtype,s="ss"===r||"as"===r?r:void 0;n.push({id:e.id,polymerType:e.polymerType,backboneAtoms:e.backboneAtoms,bonds:e.bonds,...void 0!==e.annotation?{annotation:e.annotation}:{},...void 0!==s?{strandType:s}:{}})}for(let t of e)i.push(t);let o=0;for(let e of this.chains)for(let t of e.backboneAtoms)o+=1,t.bio.continuousId=o,void 0!==t.branchAtom&&(o+=1,t.branchAtom.bio.continuousId=o);let r=[];for(let e of this.groups)r.push({id:e.id,kind:e.kind,members:e.members,...void 0!==e.repeat?{repeat:e.repeat}:{}});return{atoms:t,bonds:i,chains:n,groups:r,annotations:this.annotations}}sourceOrderAtoms(e){let t=[];for(let i of e.backboneAtoms)t.push(i),void 0!==i.branchAtom&&t.push(i.branchAtom);return t}resolveAtomByPosition(e,t,i){if("any"===t.kind)return e.backboneAtoms[0]??null;if("symbol"===t.kind){let n=e.backboneAtoms.find(e=>e.symbol===t.value);if(void 0===n){let n=e.allAtoms.find(e=>e.symbol===t.value);return void 0===n?(this.emit("warning","position-out-of-range",`Chain '${e.id}' has no monomer with symbol '${t.value}'`,i),e.backboneAtoms[0]??null):n}return n}let n=this.sourceOrderAtoms(e),o=t.value;return o<1||o>n.length?(this.emit("error","position-out-of-range",`Position ${o} out of range for chain '${e.id}' (length ${n.length})`,i),e.backboneAtoms[0]??null):n[o-1]}emit(e,t,i,n){let o={severity:e,code:t,message:i,...void 0!==n?{span:{start:n.start,end:n.end}}:{}};if(this.diagnostics.push(o),"strict"===this.mode&&"error"===e)throw new R(t,i,{...void 0!==n?{span:{start:n.start,end:n.end}}:{}})}};function qe(e,t){let i=function(e){let t=(t,i)=>t.polymerType===ne.CHEM||t.polymerType===ne.BLOB||!function(e,t,i){for(let n of i){if("backbone"!==n.kind||"numeric"!==n.r1.kind||"numeric"!==n.r2.kind)continue;let i=n.a1.id===e.id&&n.a2.id===t.id&&2===n.r1.r&&1===n.r2.r,o=n.a1.id===t.id&&n.a2.id===e.id&&2===n.r1.r&&1===n.r2.r;if(i||o)return!0}return!1}(t.backboneAtoms[i],t.backboneAtoms[i+1],e.bonds),i=!1;for(let n of e.chains){for(let e=0;e<n.backboneAtoms.length-1;e++)if(t(n,e)){i=!0;break}if(i)break}if(!i)return e;let n=new Set(e.chains.map(e=>e.id)),o=e=>{let t=1;for(;n.has(`${e}${t}`);)t+=1;let i=`${e}${t}`;return n.add(i),i},r=[];for(let i of e.chains){let e=[[]],n=e[0];for(let o=0;o<i.backboneAtoms.length;o++){let r=i.backboneAtoms[o];n.push(r),o<i.backboneAtoms.length-1&&t(i,o)&&(n=[],e.push(n))}for(let t=0;t<e.length;t++){let n={id:0===t?i.id:o(i.polymerType),polymerType:i.polymerType,atoms:e[t]};0===t&&void 0!==i.annotation&&(n.annotation=i.annotation),r.push(n)}}let s=new Map;for(let e of r)for(let t=0;t<e.atoms.length;t++){let i=e.atoms[t];s.set(i.id,{chainId:e.id,pos:t+1}),void 0!==i.branchAtom&&s.set(i.branchAtom.id,{chainId:e.id,pos:t+1})}let a=new Map;for(let t of e.atoms){let e=s.get(t.id);void 0===e||t.bio.chainId===e.chainId&&t.bio.positionInChain===e.pos?a.set(t.id,t):a.set(t.id,{...t,bio:{...t.bio,chainId:e.chainId,positionInChain:e.pos}})}for(let t of e.atoms){if(void 0===t.branchAtom)continue;let e=a.get(t.id),i=a.get(t.branchAtom.id);void 0===e||void 0===i||(e.branchAtom=i)}let l=e.bonds.map(e=>{let t=a.get(e.a1.id)??e.a1,i=a.get(e.a2.id)??e.a2;return t===e.a1&&i===e.a2?e:{...e,a1:t,a2:i}}),h=r.map(e=>{let t=e.atoms.map(e=>a.get(e.id)??e),i=new Set;for(let t of e.atoms)i.add(t.id),void 0!==t.branchAtom&&i.add(t.branchAtom.id);let n=[];for(let e of l)i.has(e.a1.id)&&i.has(e.a2.id)&&n.push(e);return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:n,...void 0!==e.annotation?{annotation:e.annotation}:{}}});return{atoms:e.atoms.map(e=>a.get(e.id)??e),bonds:l,chains:h,groups:e.groups,annotations:e.annotations}}(e);return new je(i,t??{}).emit()}var je=class{constructor(e,t){this.mol=e,this.options=t}emit(){return`${this.orderedChains().map(e=>this.emitPolymer(e)).join("|")}$${this.emitConnections()}$${this.emitGroupsAndBondRatios()}$${this.emitAnnotations()}${this.versionTrailer()}`}orderedChains(){if(!0!==this.options.canonicalize)return this.mol.chains;let e=this.mol.chains.slice();return e.sort((e,t)=>e.polymerType!==t.polymerType?e.polymerType<t.polymerType?-1:1:e.id<t.id?-1:e.id>t.id?1:0),e}emitPolymer(e){let t=this.emitChainBody(e),i=void 0!==e.annotation?`"${Ve(e.annotation)}"`:"";return`${e.id}{${t}}${i}`}emitChainBody(e){switch(e.polymerType){case"PEPTIDE":return this.emitPeptideBody(e);case"RNA":return this.emitRnaBody(e);case"CHEM":return this.emitChemBody(e);case"BLOB":return this.emitBlobBody(e);default:return""}}emitPeptideBody(e){let t=this.bracketsForChain(e.id),i=[],n=0,o=0,r=null;for(;n<e.backboneAtoms.length;){let s=e.backboneAtoms[n],a=t.find(e=>e.startAtomId===s.id);void 0!==a&&null===r&&(i.push("("),r=a,o+=1),i.push(this.emitMonomerToken(s));let l=void 0!==s.tag?`"${Ve(s.tag)}"`:"";i.push(l),null!==r&&r.endAtomId===s.id&&(i.push(`)${Ye(r.min,r.max)}`),r=null,o-=1),n+=1,n<e.backboneAtoms.length&&i.push(".")}return i.join("")}emitRnaBody(e){let t=this.bracketsForChain(e.id),i=[],n=0,o=!0,r=null,s=e=>{null!==r&&r.endAtomId===e&&(i.push(`)${Ye(r.min,r.max)}`),r=null)},a=e=>{let n=t.find(t=>t.startAtomId===e);void 0!==n&&null===r&&(i.push("("),r=n)};for(;n<e.backboneAtoms.length;){let t=e.backboneAtoms[n];if(o||i.push("."),o=!1,t.biotype!==ie){if(t.biotype===Q){a(t.id),i.push(this.emitMonomerToken(t)),void 0!==t.tag&&i.push(`"${Ve(t.tag)}"`),void 0!==t.branchAtom&&(i.push("("),i.push(this.emitMonomerToken(t.branchAtom)),void 0!==t.branchAtom.tag&&i.push(`"${Ve(t.branchAtom.tag)}"`),i.push(")"));let o=e.backboneAtoms[n+1];void 0!==o&&o.biotype===J?(i.push(this.emitMonomerToken(o)),void 0!==o.tag&&i.push(`"${Ve(o.tag)}"`),s(o.id),n+=2):(s(t.id),n+=1);continue}a(t.id),i.push(this.emitMonomerToken(t)),void 0!==t.tag&&i.push(`"${Ve(t.tag)}"`),s(t.id),n+=1}else a(t.id),i.push(this.emitMonomerToken(t)),void 0!==t.tag&&i.push(`"${Ve(t.tag)}"`),s(t.id),n+=1}return i.join("")}emitChemBody(e){let t=e.backboneAtoms[0];if(void 0===t)return"";let i=void 0!==t.tag?`"${Ve(t.tag)}"`:"";return`${this.emitMonomerToken(t)}${i}`}emitBlobBody(e){let t=e.backboneAtoms[0];if(void 0===t)return"";let i=void 0!==t.tag?`"${Ve(t.tag)}"`:"";return`${this.emitMonomerToken(t)}${i}`}emitMonomerToken(e){let t;return t=void 0!==e.inlineSource?`[${e.inlineSource}]`:void 0===e.bio.ambiguity||"?"!==e.symbol&&!e.bio.ambiguity.startsWith("(")?e.symbol:e.bio.ambiguity,!0===this.options.includeHighlights&&e.selected?`<span style='background:#bbf;'>${t}</span>`:t}emitConnections(){let e=[];for(let t of this.crossPolymerBonds())e.push(this.emitConnection(t));return e.join("|")}*crossPolymerBonds(){let e=new Map;for(let t of this.mol.chains){let i=new Map;for(let e=0;e<t.backboneAtoms.length;e++)i.set(t.backboneAtoms[e].id,e);e.set(t.id,i)}for(let t of this.mol.bonds)if("backbone"!==t.kind)if("branch"!==t.kind)yield t;else{if(void 0!==t.a1.branchAtom&&t.a1.branchAtom.id===t.a2.id||void 0!==t.a2.branchAtom&&t.a2.branchAtom.id===t.a1.id)continue;yield t}else{if(t.a1.bio.chainId===t.a2.bio.chainId){let i=e.get(t.a1.bio.chainId);if(void 0!==i){let e=i.get(t.a1.id),n=i.get(t.a2.id);if(void 0!==e&&void 0!==n&&1===Math.abs(e-n))continue}}yield t}}emitConnection(e){let t=We(e.r1,e.kind),i=We(e.r2,e.kind),n=void 0!==e.tag?`"${Ve(e.tag)}"`:"",o=String(this.connectionPosition(e.a1)),r=String(this.connectionPosition(e.a2));return`${e.a1.bio.chainId},${e.a2.bio.chainId},${o}:${t}-${r}:${i}${n}`}connectionPosition(e){return K(e,this.mol.chains.find(t=>t.id===e.bio.chainId))}emitGroupsAndBondRatios(){let e=[];for(let t of this.mol.groups)"bracket"!==t.kind&&e.push(this.emitGroup(t));for(let t of this.mol.bonds){if("cross-polymer"!==t.kind||void 0===t.ratio)continue;let i=void 0!==t.ratio.denominator?`${t.ratio.numerator}/${t.ratio.denominator}`:`${t.ratio.numerator}`;e.push(`${t.a1.bio.chainId}+${t.a2.bio.chainId}:${i}`)}return e.join("|")}emitGroup(e){let t="and"===e.kind?"+":",",i=e.members.map(e=>{return void 0===(t=e).ratio?t.target:`${t.target}:${t.ratio}`;var t}).join(t);return`${e.id}(${i})`}emitAnnotations(){let e=this.mol.annotations.perPolymer;if(0===e.size)return"";let t={};for(let[i,n]of e)t[i]=n;return JSON.stringify(t)}versionTrailer(){let e=this.options.version??"V2.0";if("none"===e)return"";if("preserve"===e){let e=this.mol.annotations.version;return""===e?"":`$${e}`}return`$${e}`}bracketsForChain(e){let t=[],i=new Map;for(let e of this.mol.atoms)i.set(e.id,e.bio.chainId);for(let n of this.mol.groups){if("bracket"!==n.kind)continue;let o=[];for(let e of n.members){let t=parseInt(e.target,10);Number.isFinite(t)&&o.push(t)}if(0===o.length)continue;let r=new Set;for(let e of o){let t=i.get(e);void 0!==t&&r.add(t)}if(!r.has(e)||r.size>1)continue;let s=n.repeat??{min:1,max:1};t.push({members:o,min:s.min,max:s.max,set:new Set(o),startAtomId:o[0],endAtomId:o[o.length-1]})}return t}};function Ve(e){let t="";for(let i=0;i<e.length;i++){let n=e.charCodeAt(i);t+=34!==n?92!==n?10!==n?13!==n?9!==n?e.charAt(i):"\\t":"\\r":"\\n":"\\\\":'\\"'}return t}function Ye(e,t){return e===t?`'${e}'`:`'${e}-${t}'`}function We(e,t){switch(e.kind){case"numeric":return`R${e.r}`;case"unspecified":default:return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${e.position}:R${e.r}`}}var Ue=class{constructor(e){this.chainIdMap=new Map,this.mol=e}run(){let e=this.mol.chains.slice().sort((e,t)=>e.polymerType!==t.polymerType?e.polymerType<t.polymerType?-1:1:Qe(e.id,t.id)),t={},i=[];for(let n of e){let e=Ke(n.polymerType);t[e]=(t[e]??0)+1;let o=`${e}${t[e]}`;this.chainIdMap.set(n.id,o),i.push(n)}let n=new Map;for(let e of this.mol.atoms){let t=this.chainIdMap.get(e.bio.chainId)??e.bio.chainId;n.set(e.id,{...e,bio:{...e.bio,chainId:t}})}for(let e of this.mol.atoms){if(void 0===e.branchAtom)continue;let t=n.get(e.id),i=n.get(e.branchAtom.id);void 0!==t&&void 0!==i&&(t.branchAtom=i)}let o=this.mol.bonds.map(e=>({...e,a1:n.get(e.a1.id)??e.a1,a2:n.get(e.a2.id)??e.a2})),r=new Map;for(let e of o)r.set(e.id,e);let s=i.map(e=>{let t=this.chainIdMap.get(e.id)??e.id,i=[];for(let t of e.backboneAtoms){let e=n.get(t.id);void 0!==e&&i.push(e)}let o=[];for(let t of e.bonds){let e=r.get(t.id);void 0!==e&&o.push(e)}return{id:t,polymerType:e.polymerType,backboneAtoms:i,bonds:o,...void 0!==e.annotation&&e.annotation.length>0?{annotation:e.annotation}:{}}}),a=new Map;for(let e of s)a.set(e.id,e);o.sort((e,t)=>{let i=Xe(e.kind),n=Xe(t.kind);if(i&&!n)return 1;if(!i&&n)return-1;if(!i&&!n)return e.id-t.id;let o=e.a1.bio.chainId,r=t.a1.bio.chainId;if(o!==r)return o<r?-1:1;let s=e.a2.bio.chainId,l=t.a2.bio.chainId;if(s!==l)return s<l?-1:1;let h=K(e.a1,a.get(e.a1.bio.chainId)),d=K(t.a1,a.get(t.a1.bio.chainId));return h!==d?h-d:K(e.a2,a.get(e.a2.bio.chainId))-K(t.a2,a.get(t.a2.bio.chainId))});let l=this.renumberGroups(this.mol.groups),h=this.rekeyAnnotations(this.mol.annotations);return{atoms:this.mol.atoms.map(e=>n.get(e.id)),bonds:o,chains:s,groups:l,annotations:h}}renumberGroups(e){let t=[],i=[];for(let n of e)"bracket"===n.kind?t.push(this.rekeyBracket(n)):i.push(n);i.sort((e,t)=>Qe(e.id,t.id));let n={G:0};return i.map(e=>{n.G+=1;let t=`G${n.G}`;return{...e,id:t,members:e.members.map(e=>this.rekeyMember(e))}}).concat(t)}rekeyBracket(e){return e}rekeyMember(e){let t=this.chainIdMap.get(e.target);return void 0===t?e:void 0===e.ratio?{target:t}:{target:t,ratio:e.ratio}}rekeyAnnotations(e){let t=new Map;for(let[i,n]of e.perPolymer){let e=this.chainIdMap.get(i)??i;0!==Object.keys(n).length&&t.set(e,n)}return{perPolymer:t,version:e.version}}};function Ke(e){switch(e){case"PEPTIDE":return"PEPTIDE";case"RNA":return"RNA";case"CHEM":return"CHEM";default:return"BLOB"}}function Xe(e){return"cross-polymer"===e||"hbond"===e}function Qe(e,t){let i=/^([A-Z]+)([0-9]+)$/.exec(e),n=/^([A-Z]+)([0-9]+)$/.exec(t);return null===i||null===n?e<t?-1:e>t?1:0:i[1]!==n[1]?i[1]<n[1]?-1:1:parseInt(i[2],10)-parseInt(n[2],10)}function Ze(e,t){let i=[...e.atoms],n=i[0];for(let e of i)for(let i of t.get(e)??[])if("hbond"===i.kind)throw new N("gap-at-complex-junction",`Gap atom ${e} participates in a hydrogen bond`,{atomId:e});if(e.boundary.length>2)throw new N("gap-at-complex-junction",`Gap atom ${n} sits at a junction of ${e.boundary.length} connections (max 2 allowed)`,{atomId:n,bondCount:e.boundary.length});if(2===e.boundary.length){let t=Je(e,e.boundary[0]),i=Je(e,e.boundary[1]);if(t.atom.id===i.atom.id)throw new N("gap-at-complex-junction",`Removing gap atom ${n} would bond monomer '${t.atom.symbol}' to itself`,{atomId:n})}}function Je(e,t){return e.atoms.has(t.a1.id)?{atom:t.a2,r:t.r2}:{atom:t.a1,r:t.r1}}function et(e,t){return"numeric"===e.kind&&e.r===t}var tt=[function(e,t){let i=[],n=new Set(e.chains.map(e=>e.id));for(let t of e.bonds)"cross-polymer"!==t.kind&&"hbond"!==t.kind||(n.has(t.a1.bio.chainId)||i.push({severity:"error",code:"unknown-chain-reference",message:`Connection references unknown chain '${t.a1.bio.chainId}'`,context:{chainId:t.a1.bio.chainId,bondId:t.id}}),n.has(t.a2.bio.chainId)||i.push({severity:"error",code:"unknown-chain-reference",message:`Connection references unknown chain '${t.a2.bio.chainId}'`,context:{chainId:t.a2.bio.chainId,bondId:t.id}}));for(let t of e.chains)for(let n of e.bonds){if("cross-polymer"!==n.kind&&"hbond"!==n.kind)continue;let e=0;for(let i of t.backboneAtoms)e+=void 0!==i.branchAtom?2:1;for(let o of[n.a1,n.a2]){if(o.bio.chainId!==t.id)continue;let n=K(o,t);(n<1||n>e)&&i.push({severity:"error",code:"position-out-of-range",message:`Position ${n} out of range for chain '${t.id}' (length ${e})`,context:{chainId:t.id,atomId:o.id,found:n}})}}let o=new Set;for(let t of e.groups)"bracket"!==t.kind&&o.add(t.id);for(let t of e.groups)if("bracket"!==t.kind)for(let e of t.members)n.has(e.target)||o.has(e.target)||i.push({severity:"error",code:"unknown-group-reference",message:`Group '${t.id}' references unknown id '${e.target}'`,context:{found:e.target}});let r=new Map;for(let t of e.groups){if("bracket"===t.kind)continue;let e=[];for(let i of t.members)o.has(i.target)&&e.push(i.target);r.set(t.id,e)}for(let e of r.keys()){let t=new Set,n=[e];for(;n.length>0;){let o=n.pop();if(t.has(o))continue;t.add(o);let s=r.get(o)??[];for(let o of s)o===e?i.push({severity:"error",code:"group-cycle",message:`Group cycle detected involving '${e}'`,context:{found:e}}):t.has(o)||n.push(o)}}return i},function(e,t){let i=[];if(null===t)return i;let n=new Map;for(let t of e.chains)n.set(t.id,t.polymerType);for(let t of e.atoms){let e=n.get(t.bio.chainId);if(void 0===e)continue;let o=t.monomer,r=o?.meta;null!==o&&!0!==r?.missing?!0!==r?.ambiguous&&void 0!==o.smiles&&o.smiles.length>0&&(0===o.rgroups.length?i.push({severity:"warning",code:"inline-smiles-without-r-groups",message:`Inline-SMILES monomer '${o.symbol}' has no R-groups`,context:{atomId:t.id,found:o.symbol}}):o.rgroups.length>4&&i.push({severity:"warning",code:"inline-smiles-too-many-rs",message:`Inline-SMILES monomer '${o.symbol}' has ${o.rgroups.length} R-groups (max 4 expected)`,context:{atomId:t.id,found:o.rgroups.length}})):i.push({severity:"warning",code:"unresolved-monomer",message:`Monomer '${t.symbol}' not found in library for ${e}`,context:{chainId:t.bio.chainId,atomId:t.id,found:t.symbol}})}for(let o of e.atoms){let e=n.get(o.bio.chainId);if(void 0!==e&&null===t.getMonomer(e,o.symbol))for(let n of t.getMonomerSymbolsByType(e))if(n!==o.symbol&&n.toLowerCase()===o.symbol.toLowerCase()){i.push({severity:"info",code:"case-mismatch",message:`Symbol '${o.symbol}' differs from library entry '${n}' only in case`,context:{atomId:o.id,found:o.symbol,expected:n}});break}}return i},function(e,t){let i=[],n=new Map;for(let t of e.bonds)for(let[e,o]of[[t.a1,t.r1],[t.a2,t.r2]]){if("numeric"!==o.kind)continue;let r=n.get(e.id)??new Set;r.has(o.r)&&i.push({severity:"error",code:"rgroup-already-bonded",message:`R-group R${o.r} on atom ${e.id} already bonded`,context:{atomId:e.id,bondId:t.id,found:o.r}}),r.add(o.r),n.set(e.id,r)}for(let t of e.bonds){for(let[e,n]of[[t.a1,t.r1],[t.a2,t.r2]]){if("numeric"!==n.kind||null===e.monomer)continue;let o=e.monomer.rs;(n.r<1||n.r>o)&&i.push({severity:"error",code:"rgroup-not-on-monomer",message:`R-group R${n.r} not defined on monomer '${e.symbol}' (rs=${o})`,context:{atomId:e.id,bondId:t.id,found:n.r,expected:`R1..R${o}`}})}"backbone"===t.kind&&"numeric"===t.r1.kind&&"numeric"===t.r2.kind&&(2===t.r1.r&&1===t.r2.r||i.push({severity:"warning",code:"backbone-rgroup-misaligned",message:`Backbone bond uses R${t.r1.r}->R${t.r2.r} (expected R2->R1)`,context:{bondId:t.id,found:`R${t.r1.r}->R${t.r2.r}`}})),"branch"===t.kind&&"numeric"===t.r1.kind&&3!==t.r1.r&&i.push({severity:"warning",code:"branch-rgroup-misaligned",message:`Branch bond uses R${t.r1.r} (expected R3 on parent)`,context:{bondId:t.id,found:`R${t.r1.r}`}})}for(let t of e.atoms){if(null===t.monomer)continue;let e=n.get(t.id)?.size??0;if(t.monomer.rs>e){let n=t.monomer.rs-e;n>0&&t.monomer.rs>0&&i.push({severity:"info",code:"unmatched-r-group",message:`Monomer '${t.symbol}' on atom ${t.id} has ${n} unused R-group(s); default cap applied`,context:{atomId:t.id,found:n}})}}return i},function(e,t){let i=[];for(let t of e.chains){if("CHEM"===t.polymerType&&t.backboneAtoms.length>1&&i.push({severity:"error",code:"chem-multiple-monomers",message:`CHEM polymer '${t.id}' has ${t.backboneAtoms.length} monomers (expected 1)`,context:{chainId:t.id,found:t.backboneAtoms.length}}),"BLOB"===t.polymerType)for(let e of t.backboneAtoms)void 0===e.bio.blobtype&&"Bead"!==e.symbol&&"Group"!==e.symbol&&i.push({severity:"error",code:"blob-non-blob-symbol",message:`BLOB '${t.id}' contains non-blob symbol '${e.symbol}'`,context:{chainId:t.id,atomId:e.id,found:e.symbol}});if("RNA"===t.polymerType){let e=!1;for(let n=0;n<t.backboneAtoms.length;n++){let o=t.backboneAtoms[n];o.biotype===Z&&!e&&i.push({severity:"error",code:"rna-bare-base",message:`Bare base '${o.symbol}' without parent sugar in '${t.id}'`,context:{chainId:t.id,atomId:o.id}}),o.biotype===J&&(t.backboneAtoms.slice(0,n).some(e=>e.biotype===Q)||i.push({severity:"warning",code:"rna-bare-linker",message:`Bare linker '${o.symbol}' before any sugar in '${t.id}'`,context:{chainId:t.id,atomId:o.id}})),e=o.biotype===Q||o.biotype===J}}}return i},function(e,t){let i=[],n=new Map;for(let t of e.chains)n.set(t.id,t.polymerType);let o=new Map;for(let t of e.bonds){if("hbond"!==t.kind)continue;o.set(t.a1.id,(o.get(t.a1.id)??0)+1),o.set(t.a2.id,(o.get(t.a2.id)??0)+1);let e=n.get(t.a1.bio.chainId),r=n.get(t.a2.bio.chainId);("RNA"!==e||"RNA"!==r)&&i.push({severity:"error",code:"pair-non-rna",message:`Hydrogen-bond connects non-RNA chains (${e}/${r})`,context:{bondId:t.id}}),(t.a1.biotype!==Z||t.a2.biotype!==Z)&&i.push({severity:"warning",code:"pair-position-not-base",message:"Hydrogen-bond endpoints are not both bases",context:{bondId:t.id,found:`${t.a1.biotype}/${t.a2.biotype}`}}),it(t.a1.symbol,t.a2.symbol)||i.push({severity:"warning",code:"pair-non-canonical",message:`Non-canonical pair ${t.a1.symbol}-${t.a2.symbol}`,context:{bondId:t.id,found:`${t.a1.symbol}-${t.a2.symbol}`}})}for(let[e,t]of o)t>1&&i.push({severity:"warning",code:"pair-already-paired",message:`Base atom ${e} participates in ${t} pair bonds`,context:{atomId:e,found:t}});return i},function(e,t){let i=[];for(let t of e.atoms){let e=t.bio.ambiguity;if(void 0!==e)if("and"===t.bio.ambiguityKind){let n=nt(e,"+");for(let e of n)void 0!==e.ratio&&e.ratio<0&&i.push({severity:"error",code:"ratio-and-negative",message:`AND ratio for '${e.symbol}' is negative (${e.ratio})`,context:{atomId:t.id,found:e.ratio}})}else if("or"===t.bio.ambiguityKind){let n=nt(e,","),o=0,r=!1;for(let e of n)"number"==typeof e.ratio&&(o+=e.ratio,r=!0);r&&Math.abs(o-1)>.001&&Math.abs(o-100)>.5&&i.push({severity:"info",code:"ratio-doesnt-sum-to-1",message:`OR ratios sum to ${o} (expected 1.0 or 100)`,context:{atomId:t.id,found:o}})}}return i},function(e,t){let i=[],n=new Set(e.chains.map(e=>e.id));for(let t of e.annotations.perPolymer.keys())n.has(t)||i.push({severity:"warning",code:"annotation-unknown-polymer",message:`Annotation references unknown polymer '${t}'`,context:{found:t}});return i},function(e,t){let i=[];for(let t of e.chains)t.backboneAtoms.length>1e4&&i.push({severity:"info",code:"polymer-too-long",message:`Polymer '${t.id}' has ${t.backboneAtoms.length} atoms (> 10000); renderer may switch to rows layout`,context:{chainId:t.id,found:t.backboneAtoms.length}});let n=0;for(let t of e.bonds)("cross-polymer"===t.kind||"hbond"===t.kind)&&(n+=1);n>1e3&&i.push({severity:"info",code:"connection-count-high",message:`${n} cross-polymer/hbond connections (> 1000); rendering may be slow`,context:{found:n}});for(let t of e.groups)"bracket"===t.kind&&void 0!==t.repeat&&t.repeat.max>1e4&&i.push({severity:"warning",code:"bracket-repeat-too-large",message:`Bracket repeat upper bound ${t.repeat.max} > 10000`,context:{found:t.repeat.max}});return i}];function it(e,t){let i=e.toUpperCase(),n=t.toUpperCase();return new Set(["A:T","T:A","A:U","U:A","G:C","C:G"]).has(`${i}:${n}`)}function nt(e,t){let i=e.trim();i.startsWith("(")&&i.endsWith(")")&&(i=i.slice(1,-1));let n=i.split(t),o=[];for(let e of n){let t=e.trim();if(0===t.length)continue;let i=t.indexOf(":");if(i<0){o.push({symbol:t});continue}let n=t.slice(0,i),r=t.slice(i+1),s=parseFloat(r);Number.isFinite(s)?o.push({symbol:n,ratio:s}):o.push({symbol:n})}return o}function ot(e){let t=new Map;for(let i of e)t.set(i.polymerType,(t.get(i.polymerType)??0)+i.backbone.length);let i=e[0].polymerType,n=-1;for(let o of e){let e=t.get(o.polymerType);e>n&&(i=o.polymerType,n=e)}return i}function rt(e,t,i){let n=(e,t)=>"numeric"===e.kind&&e.r===t,o=[[e.a1,e.r1,e.a2,e.r2],[e.a2,e.r2,e.a1,e.r1]];for(let[e,r,s,a]of o){if(!n(r,2)||!n(a,1))continue;let o=i.get(e.id),l=i.get(s.id);if(void 0===o||void 0===l)continue;let h=t[o],d=t[l];if(h.backbone[h.backbone.length-1].id===e.id&&d.backbone[0].id===s.id)return{tail:o,head:l}}return null}function st(e,t,i){let n=new Set,o=t;for(;void 0!==o&&!n.has(o);){if(o===i)return!0;n.add(o),o=e.get(o)}return!1}function at(e){switch(e){case ne.PEPTIDE:return"PEPTIDE";case ne.RNA:return"RNA";case ne.CHEM:return"CHEM";default:return"BLOB"}}function lt(e,t,i,n){if(i.length<2)return!1;let o=i[0],r=i[i.length-1];for(let i of e.bonds){if("backbone"===i.kind||"branch"===i.kind)continue;let e=n.get(i.a1.id),s=n.get(i.a2.id);if(e!==t||s!==t||!(i.a1.id===r.id&&i.a2.id===o.id||i.a2.id===r.id&&i.a1.id===o.id))continue;let a=i.a1.id===o.id?i.r1:i.r2,l=i.a1.id===r.id?i.r1:i.r2,h="numeric"===a.kind&&1===a.r,d="numeric"===l.kind&&2===l.r;if(h&&d)return!0}return!1}var ht=44.800000000000004,dt=42/ht,ct=42/ht,ut=42/ht;function pt(e,t){let i=t?.bondLength??28,n=t?.origin??{x:0,y:0},o=1.6*i,r=new Map;for(let t=0;t<e.backbone.length;t++){let i=e.backbone[t];r.set(i.id,{x:n.x+t*o,y:n.y})}return r}var mt=Math.PI/180;function ft(e,t){let i=e.backbone.length;if(i<=2){let i={};return void 0!==t?.bondLength&&(i.bondLength=t.bondLength),void 0!==t?.origin&&(i.origin=t.origin),pt(e,i)}let n=t?.bondLength??28,o=t?.origin??{x:0,y:0},r=t?.startDegrees??-90,s=1.6*n/(2*Math.sin(Math.PI/i)),a=new Map;for(let t=0;t<i;t++){let n=e.backbone[t],l=(r+360*t/i)*mt;a.set(n.id,{x:o.x+s*Math.cos(l),y:o.y+s*Math.sin(l)})}return a}function bt(e,t){let i=new Map;for(let t=0;t<e.backbone.length;t++)i.set(e.backbone[t].id,t);let n=e.backbone.length-1,o=[];for(let e of t.bonds){if("backbone"===e.kind||"branch"===e.kind)continue;let t=i.get(e.a1.id),r=i.get(e.a2.id);if(void 0===t||void 0===r)continue;let s=Math.min(t,r),a=Math.max(t,r);a-s<2||0===s&&a===n&&gt(e)||o.push({lo:s,hi:a})}return o}function gt(e){let t=[e.r1,e.r2].filter(e=>"numeric"===e.kind).map(e=>e.r);return 2===t.length&&t.includes(1)&&t.includes(2)}function At(e,t,i){if(null===t)return pt(e,i);let n=i?.bondLength??28,o=i?.origin??{x:0,y:0},r=1.6*n,s=bt(e,t);if(0===s.length)return pt(e,i);let a=s[0].lo,l=s[0].hi;for(let e of s)e.lo<a&&(a=e.lo),e.hi>l&&(l=e.hi);let h=e.backbone.slice(a,l+1),d=h.length,c=r/(2*Math.sin(Math.PI/d)),u={id:e.id,polymerType:e.polymerType,segments:e.segments,backbone:h,bases:new Array(d).fill(null),baseBonds:new Array(d).fill(null)},p=a,m={x:o.x+p*r+c,y:o.y},f=ft(u,{bondLength:n,origin:m,startDegrees:180}),b=new Map;for(let t=0;t<a;t++){let i=e.backbone[t];b.set(i.id,{x:o.x+t*r,y:o.y})}for(let[e,t]of f)b.set(e,t);let g=h[d-1],A=f.get(g.id)??m,_=A.x-m.x,y=A.y-m.y,v=Math.hypot(_,y);v<1e-6&&(_=0,y=1,v=1);let w=_/v,x=y/v,C={x:A.x+w*r,y:A.y+x*r},E=Math.sign(A.x-m.x);if(0===E&&d>=2){let e=f.get(h[d-2].id);void 0!==e&&(E=Math.sign(A.x-e.x))}0===E&&(E=1);for(let t=l+1;t<e.backbone.length;t++){let i=e.backbone[t],n=t-(l+1);b.set(i.id,0===n?C:{x:C.x+E*r*n,y:C.y})}return b}function _t(e){let t=new Map,i=new Map;for(let n=0;n<e.backbone.length;n++){t.set(e.backbone[n].id,n);let o=e.bases[n];null!=o&&i.set(o.id,n)}return{sugarToIdx:t,baseToIdx:i}}function yt(e,t,i){let n=t.get(e);if(void 0!==n)return n;let o=i.get(e);return void 0!==o?o:null}function vt(e,t,i){let n="hbond"===e.kind,o="cross-polymer"===e.kind&&"object"==typeof e.r1&&null!==e.r1&&"pair"===e.r1.kind&&"object"==typeof e.r2&&null!==e.r2&&"pair"===e.r2.kind;if(!n&&!o)return null;let r=yt(e.a1.id,t,i),s=yt(e.a2.id,t,i);return null===r||null===s||r===s?null:{lo:Math.min(r,s),hi:Math.max(r,s)}}function wt(e){let t=Math.hypot(e.x,e.y);return 0===t?{x:1,y:0}:{x:e.x/t,y:e.y/t}}function xt(e,t,i){return{x:e.x+t*Math.cos(i),y:e.y+t*Math.sin(i)}}function Ct(e,t,i,n,o){let r=o.chain.bases[e];null!=r&&o.out.set(r.id,{x:t.x+n*i.x,y:t.y+n*i.y})}function Et(e,t,i){let{chain:n,step:o,rail:r,baseInwardHang:s,out:a}=i,l=2*e.numPairs-1,h={x:t.normal.x,y:t.normal.y},d={x:-t.normal.x,y:-t.normal.y};for(let c=0;c<l;c++){let l=n.backbone[e.fromIdx+c],u=n.backbone[e.toIdx-c],p=c*o,m={x:t.origin.x+p*t.tangent.x,y:t.origin.y+p*t.tangent.y},f={x:t.origin.x+p*t.tangent.x+r*t.normal.x,y:t.origin.y+p*t.tangent.y+r*t.normal.y};a.set(l.id,m),a.set(u.id,f),Ct(e.fromIdx+c,m,h,s,i),Ct(e.toIdx-c,f,d,s,i)}let c=(l-1)*o;return{origin:{x:t.origin.x+c*t.tangent.x,y:t.origin.y+c*t.tangent.y},tangent:t.tangent,normal:t.normal}}function kt(e,t,i,n){if(null===e.closingPair)return;let{step:o,rail:r,out:s}=i,a=0,l=0;for(let t of e.nodes)"unpaired"===t.kind?a+=t.to-t.from+1:l+=1;let h=function(e,t,i,n){let o=i+n+1;if(o<=0)return Math.max(e/2+1,t);let r=n+1,s=o*t,a=Math.max(s/(2*Math.PI),e/2+1);for(let t=0;t<64;t++){let t=e/(2*a),i=2*Math.asin(Math.min(.9999,Math.max(-.9999,t))),n=(2*Math.PI-r*i)*a-s,o=t,l=-e/(2*a*a)/Math.sqrt(Math.max(1e-12,1-o*o))*2,h=2*Math.PI-r*i-r*a*l;if(!Number.isFinite(h)||Math.abs(h)<1e-12)break;let d=n/h,c=a-d;if(!Number.isFinite(c)||c<e/2+.001){a=e/2+.001;break}if(a=c,Math.abs(d)<1e-9)break}return Math.max(a,e/2+.001)}(r,o,a,l),d=s.get(i.chain.backbone[e.closingPair[0]].id),c=s.get(i.chain.backbone[e.closingPair[1]].id),u=(d.x+c.x)/2,p=(d.y+c.y)/2,m=Math.sqrt(Math.max(0,h*h-r/2*(r/2))),f={x:u+m*t.tangent.x,y:p+m*t.tangent.y},b=Math.atan2(d.y-f.y,d.x-f.x),g=Math.atan2(c.y-f.y,c.x-f.x)-b;for(;g>Math.PI;)g-=2*Math.PI;for(;g<=-Math.PI;)g+=2*Math.PI;let A=g>0?-1:1,_=2*Math.asin(Math.min(.9999,Math.max(-.9999,r/(2*h)))),y=o/h,v=b;for(let t of e.nodes)if("unpaired"===t.kind)for(let e=t.from;e<=t.to;e++){v+=A*y;let t=xt(f,h,v);s.set(i.chain.backbone[e].id,t),Ct(e,t,wt({x:t.x-f.x,y:t.y-f.y}),i.step,i)}else{v+=A*y;let e=xt(f,h,v);v+=A*_;let n=xt(f,h,v);s.set(i.chain.backbone[t.fromIdx].id,e),s.set(i.chain.backbone[t.toIdx].id,n);let o=Et(t,{origin:e,tangent:wt({x:(e.x+n.x)/2-f.x,y:(e.y+n.y)/2-f.y}),normal:wt({x:n.x-e.x,y:n.y-e.y})},i);kt(t.child,o,i)}}function Bt(e,t,i){let n=1.6*(i?.bondLength??28);for(let i=0;i<e.backbone.length;i++){let o=e.bases[i];if(null==o||t.has(o.id))continue;let r=e.backbone[i],s=t.get(r.id);if(void 0===s)continue;let a=St(e,i,t);t.set(o.id,{x:s.x+n*a.x,y:s.y+n*a.y})}return t}function St(e,t,i){let n=e.backbone[t],o=i.get(n.id);if(void 0===o)return{x:0,y:1};let r=t>0?e.backbone[t-1]:void 0,s=t<e.backbone.length-1?e.backbone[t+1]:void 0,a=void 0!==r?i.get(r.id):void 0,l=void 0!==s?i.get(s.id):void 0,h=e=>{let t=e.x-o.x,i=e.y-o.y,n=Math.hypot(t,i);return n<1e-9?null:{x:t/n,y:i/n}},d=void 0!==a?h(a):null,c=void 0!==l?h(l):null;if(null!==d&&null!==c){let e=d.x+c.x,t=d.y+c.y,i=Math.hypot(e,t);if(i>.05)return{x:-e/i,y:-t/i}}let u=c??d;if(null===u)return{x:0,y:1};let 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l=e.width*a,h=e.height*a;return{x:(t-l)/2,y:(i-h)/2,width:l,height:h,scale:a}}(s,i.width,i.height,r,n.maxScale??1),l=i.x+a.x,h=i.y+a.y;return e.save(),e.beginPath(),e.rect(i.x,i.y,i.width,i.height),e.clip(),void 0!==n.backColor&&(e.fillStyle=n.backColor,e.fillRect(i.x,i.y,i.width,i.height)),e.translate(l,h),e.scale(a.scale,a.scale),e.translate(-s.x,-s.y),function(e,t,i){for(let n of t.bonds)e.save(),e.strokeStyle=Ri(n,i),e.lineWidth=Hi(),"hbond"===n.kind?e.setLineDash([4,3]):e.setLineDash([]),e.beginPath(),e.moveTo(n.a1.p.x,n.a1.p.y),e.lineTo(n.a2.p.x,n.a2.p.y),e.stroke(),e.restore()}(e,t,o),function(e,t,i,n,o=!1,r=i.bondLength){for(let s of t.atoms){if(s.hidden)continue;let t=mi(s,i),a=Ie(s.monomer,s.biotype,i.colorTheme);e.save(),e.fillStyle=a.background,e.strokeStyle=a.background,e.lineWidth=t.strokeWidth,e.lineJoin="round",e.lineCap="round","*"===s.symbol?e.setLineDash([3,3]):e.setLineDash([]),$i(e,s,t.size,t.cornerRadius??0),e.fill(),e.stroke(),e.restore();let l=s.monomer?.symbol??s.symbol;if(""!==l){let t=n*(l.length<=1?1:Math.min(1,2/l.length));e.save(),e.fillStyle=a.text,e.font=`${t}px ${i.fontFamily}`,e.textAlign="center",e.textBaseline="middle",e.fillText(l,s.p.x,s.p.y),e.restore()}if(o){let t=.525*r;e.save(),e.fillStyle=i.idColor,e.font=`${.8*n}px ${i.fontFamily}`,e.textAlign="right",e.textBaseline="bottom",e.fillText(String(s.bio.continuousId),s.p.x-t,s.p.y-t),e.restore()}}}(e,t,o,n.fontSize??o.fontSize,n.showIds??!1,n.bondLength??o.bondLength),!1!==n.showAnnotations&&function(e,t,i,n){e.save(),e.fillStyle=i.annotationColor,e.font=`${.7*n}px ${i.fontFamily}`,e.textAlign="left",e.textBaseline="alphabetic";for(let n of t.atoms){let t=n.bio.annotation;if(void 0===t||""===t)continue;let o=mi(n,i);e.fillText(t,n.p.x+o.size+2,n.p.y-o.size)}e.font=`${.8*n}px ${i.fontFamily}`;for(let n of t.chains){if(void 0===n.annotation||""===n.annotation)continue;let t=n.backboneAtoms[0];void 0!==t&&e.fillText(n.annotation,t.p.x,t.p.y-1.4*i.fontSize)}e.font=`bold ${.85*n}px ${i.fontFamily}`,e.textAlign="center",e.textBaseline="middle";let o=1.4*i.fontSize;for(let i of t.chains){if("RNA"!==i.polymerType)continue;let t=i.backboneAtoms;if(t.length<2)continue;let n=t[0],r=t[t.length-1],s=t.length>=2?t[1]:null,a=t.length>=2?t[t.length-2]:null,l=Li(n.p,s?.p??null,o),h=Li(r.p,a?.p??null,o),d=void 0!==i.strandType?`5'${i.strandType}`:"5'",c=void 0!==i.strandType?`3'${i.strandType}`:"3'";e.fillText(d,l.x,l.y),e.fillText(c,h.x,h.y)}e.restore()}(e,t,o,n.fontSize??o.fontSize),e.restore(),{bbox:{x:s.x,y:s.y,width:s.width,height:s.height},drawBox:{x:l,y:h,width:a.width,height:a.height}}}function Li(e,t,i){if(null===t)return{x:e.x-i,y:e.y};let n=e.x-t.x,o=e.y-t.y,r=Math.hypot(n,o);return 0===r?{x:e.x-i,y:e.y}:{x:e.x+i*(n/r),y:e.y+i*(o/r)}}function $i(e,t,i,n){let o=t.p,r=hi(t.biotype);switch(e.beginPath(),r){case"hexagon":Pi(e,o,6,i,-30);break;case"diamond":e.moveTo(o.x,o.y-i),e.lineTo(o.x+i,o.y),e.lineTo(o.x,o.y+i),e.lineTo(o.x-i,o.y),e.closePath();break;case"pentagon":Pi(e,o,5,i,-90);break;case"rounded-rect":case"blob":{let t=i/2,r=Math.max(0,Math.min(n,t)),s=o.x-t,a=o.y-t,l=2*t,h=2*t;e.moveTo(s+r,a),e.lineTo(s+l-r,a),e.quadraticCurveTo(s+l,a,s+l,a+r),e.lineTo(s+l,a+h-r),e.quadraticCurveTo(s+l,a+h,s+l-r,a+h),e.lineTo(s+r,a+h),e.quadraticCurveTo(s,a+h,s,a+h-r),e.lineTo(s,a+r),e.quadraticCurveTo(s,a,s+r,a),e.closePath();break}case"circle":e.ellipse(o.x,o.y,i,i,0,0,2*Math.PI)}}function Pi(e,t,i,n,o){let r=360/i;for(let s=0;s<i;s++){let i=(o+s*r)*Math.PI/180,a=t.x+n*Math.cos(i),l=t.y+n*Math.sin(i);0===s?e.moveTo(a,l):e.lineTo(a,l)}e.closePath()}function Ri(e,t){switch(e.kind){case"backbone":case"branch":case"group":return t.defaultStroke;case"cross-polymer":return t.crossPolymerBondColor;case"hbond":return function(e){if(e.a1.biotype!==Z||e.a2.biotype!==Z)return!1;let t=Di(e.a1),i=Di(e.a2);for(let[e,n]of Ni)if(t===e&&i===n||t===n&&i===e)return!0;return!1}(e)?t.hbondColor:t.nonCanonicalHbondColor}}function Hi(e){return 1.125}var Ni=[["A","T"],["A","U"],["G","C"]];function Di(e){let t=e.monomer?.naturalAnalog,i=void 0!==t&&""!==t?t:e.symbol;return 0===i.length?"":i.charAt(0).toUpperCase()}function Fi(e){let t=new Map,i=new Map;for(let t of e.bonds){let e=t.a1.id,n=t.a2.id,o=i.get(e);void 0===o&&(o=[],i.set(e,o)),o.push(t);let r=i.get(n);void 0===r&&(r=[],i.set(n,r)),r.push(t)}for(let n of e.atoms)Gi(t,n,i.get(n.id)??[]);for(let n of e.groups){if("bracket"!==n.kind)continue;let o=n.repeat?.min??1;if(1===o)continue;let r=new Set(n.members.map(e=>e.target)),s=new Map;for(let t of e.atoms){if(!r.has(t.bio.chainId))continue;let e=new Map;Gi(e,t,i.get(t.id)??[]);for(let[t,i]of e)s.set(t,(s.get(t)??0)+i*(o-1))}for(let[e,i]of s)t.set(e,(t.get(e)??0)+i)}for(let[e,i]of[...t])0===i&&t.delete(e);let n=function(e){let t=0;for(let[i,n]of e){let e=Oi[i];void 0!==e&&(t+=e*n)}return Math.round(1e3*t)/1e3}(t);return{elements:t,mw:n}}var Oi={H:1.008,C:12.011,N:14.007,O:15.999,F:18.998,Na:22.99,Mg:24.305,P:30.974,S:32.06,Cl:35.45,K:39.098,Ca:40.078,Br:79.904,I:126.904,Fe:55.845,Zn:65.38,Cu:63.546},zi={C:4,N:3,O:2,S:2,P:3,F:1,Cl:1,Br:1,I:1,H:1};function Gi(e,t,i){if(null===t.monomer)return;let n=function(e){let t=Vi.get(e);if(void 0!==t)return t;let i=function(e){let t=new Map;if(void 0===e.molfile||""===e.molfile)return{elements:t};let i=function(e){let t=e.split(/\r\n|\n|\r/);if(t.length<5)return null;let i=t[3];if(void 0===i||i.length<6)return null;let n=parseInt(i.slice(0,3),10),o=parseInt(i.slice(3,6),10);if(!Number.isFinite(n)||!Number.isFinite(o)||t.length<4+n+o)return null;let r=[];for(let e=0;e<n;e++){let i=t[4+e];if(void 0===i)return null;let n=i.slice(31,34).trim();r.push(n)}let s=new Array(n).fill(0);for(let e=0;e<o;e++){let i=t[4+n+e];if(void 0===i)return null;let o=parseInt(i.slice(0,3),10),r=parseInt(i.slice(3,6),10),a=parseInt(i.slice(6,9),10);if(!Number.isFinite(o)||!Number.isFinite(r)||!Number.isFinite(a))continue;let l=4===a?1:a;o>=1&&o<=n&&(s[o-1]=(s[o-1]??0)+l),r>=1&&r<=n&&(s[r-1]=(s[r-1]??0)+l)}return{atoms:r,bondOrders:s}}(e.molfile);if(null===i)return{elements:t};let{atoms:n,bondOrders:o}=i;for(let e=0;e<n.length;e++){let i=n[e];if("R"===i||"R#"===i||"*"===i)continue;t.set(i,(t.get(i)??0)+1);let r=zi[i];if(void 0===r)continue;let s=r-(o[e]??0);s>0&&t.set("H",(t.get("H")??0)+s)}for(let i of e.rgroups){let e=i.capGroupName;if(void 0===e)continue;let n=ji(e);for(let[e,i]of n)t.set(e,(t.get(e)??0)+i)}return{elements:t}}(e);return Vi.set(e,i),i}(t.monomer);for(let[t,i]of n.elements)e.set(t,(e.get(t)??0)+i);for(let n of i){if("hbond"===n.kind||"group"===n.kind)continue;let i=n.a1.id===t.id?n.r1:n.r2,o=qi(t.monomer,i);if(void 0===o)continue;let r=ji(o);for(let[t,i]of r)e.set(t,(e.get(t)??0)-i)}}function qi(e,t){if("numeric"!==t.kind&&"positional"!==t.kind)return;let i=(t.kind,t.r);for(let t of e.rgroups){let e=/^R([1-9][0-9]*)$/.exec(t.label);if(null!==e&&parseInt(e[1],10)===i)return t.capGroupName}}function ji(e){let t=new Map;switch(e){case"H":t.set("H",1);break;case"OH":t.set("H",1),t.set("O",1)}return t}var Vi=new WeakMap;function Yi(e){return Fi(e).mw}var Wi={AA:13.65,AC:10.67,AG:12.79,AU:12.14,CA:10.67,CC:7.52,CG:9.39,CU:8.37,GA:12.79,GC:9.39,GG:11.77,GU:10.21,UA:12.14,UC:8.37,UG:10.21,UU:8.99},Ui={A:15.4,C:7.4,G:11.7,U:10,T:8.8};function Ki(e){let t=0;for(let i of e.chains)"PEPTIDE"===i.polymerType?t+=Xi(i.backboneAtoms):"RNA"===i.polymerType&&(t+=Qi(i.backboneAtoms));return Math.round(1e4*t)/1e4}function Xi(e){let t=0,i=0,n=0;for(let o of e){let e=Zi(o);"W"===e?t++:"Y"===e?i++:"C"===e&&n++}return 5.5*t+1.49*i+.0625*n}function Qi(e){let t=[];for(let i of e)if(void 0!==i.branchAtom&&i.branchAtom.biotype===Z){let e=Zi(i.branchAtom);"T"===e&&(e="U"),""!==e&&t.push(e)}if(0===t.length)return 0;if(1===t.length){let e=t[0];return Ui[e]??0}let i=0;for(let e=0;e<t.length-1;e++){let n=t[e],o=t[e+1],r=Wi[n+o];void 0!==r&&(i+=r)}let n=0;for(let e=1;e<t.length-1;e++){let i=t[e];n+=Ui[i]??0}return 2*i-n}function Zi(e){let t=e.monomer;return null!==t&&void 0!==t.naturalAnalog&&""!==t.naturalAnalog?t.naturalAnalog.charAt(0).toUpperCase():""===e.symbol?"":e.symbol.charAt(0).toUpperCase()}function Ji(e){let t=[];t.push("HWE pseudo-molfile"),t.push(" HWE 2D"),t.push("");let i=e.atoms.length,n=e.bonds.length;t.push(function(e,t){return nn(e)+nn(t)+" 0 0 0 0 0 0 0 0999 V2000"}(i,n));for(let i of e.atoms)t.push(en(i));let o=new Map;for(let t=0;t<e.atoms.length;t++)o.set(e.atoms[t].id,t+1);for(let i of e.bonds){let e=o.get(i.a1.id),n=o.get(i.a2.id);void 0===e||void 0===n||t.push(tn(e,n))}return t.push("M END"),t.join("\n")+"\n"}function en(e){let t=function(e){let t=e.monomer;return null!==t&&""!==t.symbol?t.symbol:""!==e.symbol?e.symbol:null!==t&&void 0!==t.naturalAnalog&&""!==t.naturalAnalog?t.naturalAnalog:"X"}(e);return on(e.p.x)+on(e.p.y)+on(0)+" "+function(e){return e.length>=3?e:e+" ".repeat(3-e.length)}(t)+" 0 0 0 0 0 0 0 0 0 0 0 0"}function tn(e,t){return nn(e)+nn(t)+nn(1)+nn(0)}function nn(e){let t=String(e);return t.length>=3?t:" ".repeat(3-t.length)+t}function on(e){let t=e.toFixed(4);return t.length>=10?t.slice(0,10):" ".repeat(10-t.length)+t}var rn=new Map,sn=class{constructor(e){if(this._destroyed=!1,this._parseHits=0,this._parseMisses=0,this._layoutHits=0,this._layoutMisses=0,this._renderHits=0,this._renderMisses=0,void 0===e.monomerLib||null===e.monomerLib)throw new TypeError("HelmService: options.monomerLib is required");this.monomerLib=e.monomerLib,this.theme=e.theme??si,this.logger=e.logger??new F,this.options=Object.freeze({...e});let t=e.cacheSize??256;this._parseCache=new D({max:t}),this._layoutCache=new D({max:t}),this._renderCache=new D({max:t}),this._libUnsub=this.monomerLib.onChanged.subscribe(()=>{this.clearCaches()})}parse(e,t){this._ensureLive(),e=this._normalizeHelm(e);let i=t?.mode??"lenient",n=!1!==t?.resolveMonomers,o=`${(s={mode:i,resolveMonomers:n,helm:e}).mode}|${s.resolveMonomers?1:0}|${s.helm}`,r=this._parseCache.get(o);var s;if(void 0!==r)return this._parseHits+=1,r;this._parseMisses+=1;let a={mode:i,resolveMonomers:n},l=De(e,this.monomerLib,a),h={mol:l.mol,diagnostics:Object.freeze([...l.diagnostics])};return this._parseCache.set(o,h),h}serialize(e,t){return this._ensureLive(),qe(e,{...void 0!==t?.canonicalize?{canonicalize:t.canonicalize}:{},...void 0!==t?.includeHighlights?{includeHighlights:t.includeHighlights}:{},...void 0!==t?.version?{version:t.version}:{}})}validate(e,t){this._ensureLive(),e=this._normalizeHelm(e);let{mol:i,diagnostics:n}=this.parse(e,{mode:"lenient"}),o=void 0!==t?.mode?{mode:t.mode}:{},r=function(e,t,i){let n=i?.mode??"lenient",o=[];for(let i of tt)o.push(...i(e,t));let r="pedantic"===n?o.map(e=>"warning"===e.severity?{...e,severity:"error"}:e):o;if("strict"===n||"pedantic"===n){let e=r.filter(e=>"error"===e.severity);if(e.length>0)throw new H(e)}return r}(i,this.monomerLib,o);return[...n,...r]}canonicalize(e){this._ensureLive(),e=this._normalizeHelm(e);let{mol:t}=this.parse(e,{mode:"lenient"});return qe(new Ue(t).run(),{canonicalize:!0,version:"V2.0"})}removeGaps(e){return this._ensureLive(),function(e,t){let i=function(e){let t=new Map;for(let i of e.atoms)t.set(i.bio.continuousId,i.id);let i=new Set;for(let t of e.atoms)"*"===t.symbol&&i.add(t.id);if(0===i.size)return{mol:e,survivorByOldContinuousId:t};let n=new Map;for(let t of e.atoms)n.set(t.id,[]);for(let t of e.bonds)n.get(t.a1.id)?.push(t),t.a2.id!==t.a1.id&&n.get(t.a2.id)?.push(t);let o=function(e,t){let i=[],n=new Set;for(let o of e){if(n.has(o))continue;let r=new Set,s=[o];for(;s.length>0;){let i=s.pop();if(!r.has(i)){r.add(i),n.add(i);for(let n of t.get(i)??[]){let t=n.a1.id===i?n.a2.id:n.a1.id;e.has(t)&&!r.has(t)&&s.push(t)}}}let a=[],l=new Set;for(let e of r)for(let i of t.get(e)??[])l.has(i.id)||r.has(i.a1.id)!==r.has(i.a2.id)&&(l.add(i.id),a.push(i));i.push({atoms:r,boundary:a})}return i}(i,n);for(let e of o)Ze(e,n);let r=e.atoms.filter(e=>!i.has(e.id)),s=e.chains.map(e=>({chain:e,backbone:e.backboneAtoms.filter(e=>!i.has(e.id))})).filter(e=>e.backbone.length>0||0===e.chain.backboneAtoms.length),a=new Map,l=new Map;for(let e of s)e.backbone.forEach((t,i)=>{a.set(t.id,e.chain.id),l.set(t.id,i+1)});let h=1;for(let t of e.bonds)t.id>=h&&(h=t.id+1);let d=new Map;for(let e of o){if(2!==e.boundary.length)continue;let t=Je(e,e.boundary[0]),i=Je(e,e.boundary[1]);et(t.r,1)&&et(i.r,2)&&([t,i]=[i,t]);let n=a.get(t.atom.id)===a.get(i.atom.id),o=l.get(t.atom.id),r=l.get(i.atom.id),s=n&&void 0!==o&&void 0!==r&&o+1===r&&et(t.r,2)&&et(i.r,1)?"backbone":"cross-polymer",c=Math.min(...e.boundary.map(e=>e.id));d.set(c,{id:h++,a1:t.atom,a2:i.atom,kind:s,r1:t.r,r2:i.r})}let c=[];for(let t of e.bonds){let e=d.get(t.id);void 0!==e&&c.push(e),!i.has(t.a1.id)&&!i.has(t.a2.id)&&c.push(t)}let u=s.map(e=>({id:e.chain.id,polymerType:e.chain.polymerType,backboneAtoms:e.backbone,bonds:c.filter(t=>a.get(t.a1.id)===e.chain.id&&a.get(t.a2.id)===e.chain.id),...void 0!==e.chain.annotation?{annotation:e.chain.annotation}:{}})),p=new Map;for(let e of u){let t=0;for(let i of e.backboneAtoms)t+=1,p.set(i.id,{...i,bio:{...i.bio,positionInChain:t}})}for(let e of r)p.has(e.id)||p.set(e.id,e);for(let[e,t]of p)if(void 0!==t.branchAtom&&i.has(t.branchAtom.id)){let{branchAtom:i,...n}=t;p.set(e,n)}let m=u.map(e=>{let t=e.backboneAtoms.map(e=>p.get(e.id)),i=e.bonds.map(e=>({...e,a1:p.get(e.a1.id),a2:p.get(e.a2.id)}));return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:i,...void 0!==e.annotation?{annotation:e.annotation}:{}}}),f=c.map(e=>({...e,a1:p.get(e.a1.id),a2:p.get(e.a2.id)}));return{mol:{atoms:r.map(e=>p.get(e.id)),bonds:f,chains:m,groups:e.groups,annotations:e.annotations},survivorByOldContinuousId:t}}(De(e,t??null,{mode:"lenient",resolveMonomers:!1}).mol),n=function(e){let t=re(e),i=new Map;for(let n of e.atoms){let e=t.get(n.id);void 0!==e&&e!==n.bio.continuousId?i.set(n.id,{...n,bio:{...n.bio,continuousId:e}}):i.set(n.id,n)}for(let t of e.atoms){if(void 0===t.branchAtom)continue;let e=i.get(t.id),n=i.get(t.branchAtom.id);void 0===e||void 0===n||(e.branchAtom=n)}let n=e.bonds.map(e=>{let t=i.get(e.a1.id),n=i.get(e.a2.id);return void 0===t||void 0===n||t===e.a1&&n===e.a2?e:{...e,a1:t,a2:n}}),o=new Map;for(let e of n)o.set(e.id,e);let r=e.chains.map(e=>{let t=[];for(let n of e.backboneAtoms){let e=i.get(n.id);t.push(e??n)}let n=[];for(let t of e.bonds){let e=o.get(t.id);n.push(e??t)}return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:n,...void 0!==e.annotation?{annotation:e.annotation}:{}}});return{atoms:e.atoms.map(e=>i.get(e.id)??e),bonds:n,chains:r,groups:e.groups,annotations:e.annotations}}(i.mol),o=new Map;for(let e of n.atoms)o.set(e.id,e.bio.continuousId);let r=new Map;for(let[e,t]of i.survivorByOldContinuousId){let i=o.get(t);void 0!==i&&r.set(e,i)}return{srcHelm:e,resHelm:qe(n,{version:"V2.0"}),monomerMap:r}}(this._normalizeHelm(e),this.monomerLib)}renderToSvg(e,t){this._ensureLive(),e=this._normalizeHelm(e);let i=this._resolveRenderOptions(t),n=this._renderKey(e,i),o=this._renderCache.get(n);if(void 0!==o)return this._renderHits+=1,o;this._renderMisses+=1;let{mol:r}=this.parse(e,{mode:"lenient"}),s=this._layout(r,i.bondLength),{svg:a}=wi(s,i);return this._renderCache.set(n,a),a}renderMol(e,t){this._ensureLive();let i=this._resolveRenderOptions(t),{svg:n}=wi(e,i);return n}renderMolResult(e,t){return this._ensureLive(),wi(e,this._resolveRenderOptions(t))}async renderToPng(e,t){if(this._ensureLive(),e=this._normalizeHelm(e),"function"!=typeof globalThis.OffscreenCanvas)throw new N("png-rendering-requires-browser","HelmService.renderToPng requires OffscreenCanvas (browser-only).");let i=this._resolveRenderOptions(t),{mol:n}=this.parse(e,{mode:"lenient"});return async function(e,t={}){let i=function(){let e=globalThis;return"function"==typeof e.OffscreenCanvas?e.OffscreenCanvas:null}();if(null===i&&void 0===t.canvas)throw new Error("renderToPng: OffscreenCanvas is not available in this environment");let n=t.theme??si,o=t.width??400,r=t.height??100,s=t.pixelRatio??1,a=t.canvas??new i(Math.max(1,Math.round(o*s)),Math.max(1,Math.round(r*s))),l=a.getContext("2d");if(null===l)throw new Error("renderToPng: failed to acquire 2D context");l.save(),l.scale(s,s),Ii(l,e,{x:0,y:0,width:o,height:r},{...t,backColor:t.backColor??n.background}),l.restore();let h=a;if("function"!=typeof h.convertToBlob)throw new Error("renderToPng: canvas.convertToBlob is not available");let d=await(await h.convertToBlob({type:"image/png"})).arrayBuffer();return new Uint8Array(d)}(this._layout(n,i.bondLength),i)}renderToCanvas(e,t,i,n){this._ensureLive(),t=this._normalizeHelm(t);let o=this._resolveRenderOptions(n),{mol:r}=this.parse(t,{mode:"lenient"}),s=this._layout(r,o.bondLength),{bbox:a,drawBox:l}=Ii(e,s,i,o);return{mol:s,bbox:a,drawBox:l}}renderMolToCanvas(e,t,i,n){this._ensureLive();let o=this._resolveRenderOptions(n),{bbox:r,drawBox:s}=Ii(e,t,i,o);return{mol:t,bbox:r,drawBox:s}}*renderMany(e,t){for(let i of e??[]){let e=this.renderToSvg(i.helm,t);yield{id:i.id,svg:e}}}getFormula(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:"lenient"});return Fi(t)}getMolWeight(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:"lenient"});return Yi(t)}getExtinctionCoefficient(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:"lenient"});return Ki(t)}getMolfile(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:"lenient"});return Ji(t)}hasAtomicMolfileProvider(){return"function"==typeof this.options.atomicMolfileProvider}async getAtomicMolfile(e){this._ensureLive(),e=this._normalizeHelm(e);let t=this.options.atomicMolfileProvider;if("function"!=typeof t)throw new N("atomic-molfile-not-configured","Set HelmServiceOptions.atomicMolfileProvider to enable atomic-level expansion.");return await t(e,this.monomerLib)}hasExtraPanes(){let e=this.options.extraPanes;return void 0!==e&&e.size>0}getExtraPanes(){return this.options.extraPanes??rn}invalidate(e){if(void 0!==e)for(let t of[this._parseCache,this._layoutCache,this._renderCache]){let i=[];for(let n of t.keys())e(n)&&i.push(n);for(let e of i)t.delete(e)}else this.clearCaches()}clearCaches(){this._parseCache.clear(),this._layoutCache.clear(),this._renderCache.clear(),this._parseHits=0,this._parseMisses=0,this._layoutHits=0,this._layoutMisses=0,this._renderHits=0,this._renderMisses=0}destroy(){this._destroyed||(this._destroyed=!0,this._libUnsub(),this.clearCaches())}_ensureLive(){if(this._destroyed)throw new N("service-destroyed","HelmService instance has been destroyed.")}_normalizeHelm(e){return null==e?"":"string"==typeof e?e:String(e)}_resolveRenderOptions(e){let t={},i=e?.theme??this.theme;return t.theme=i,void 0!==e?.width&&(t.width=e.width),void 0!==e?.height&&(t.height=e.height),void 0!==e?.backColor&&(t.backColor=e.backColor),void 0!==e?.padding&&(t.padding=e.padding),void 0!==e?.showIds&&(t.showIds=e.showIds),void 0!==e?.showAnnotations&&(t.showAnnotations=e.showAnnotations),void 0!==e?.bondLength&&(t.bondLength=e.bondLength),void 0!==e?.fontSize&&(t.fontSize=e.fontSize),void 0!==e?.maxScale&&(t.maxScale=e.maxScale),void 0!==e?.showRGroupLabels&&(t.showRGroupLabels=e.showRGroupLabels),void 0!==e?.selectedAtomIds&&(t.selectedAtomIds=e.selectedAtomIds),void 0!==e?.highlightedAtomIds&&(t.highlightedAtomIds=e.highlightedAtomIds),void 0!==e?.fixedModelBbox&&(t.fixedModelBbox=e.fixedModelBbox),t}_renderKey(e,t){let i=(t.theme??this.theme).name;return`${this._libCacheTag()}|${i}|${t.width??0}x${t.height??0}|p${t.padding??-1}|b${t.bondLength??-1}|bg${t.backColor??""}|i${!0===t.showIds?1:0}a${!1===t.showAnnotations?0:1}|s${t.maxScale??1}|${e}`}_layout(e,t){let i=`${(r=e).chains.map(e=>`${e.id}:${e.polymerType}:${e.backboneAtoms.length}`).join(",")}#${r.atoms.map(e=>`${e.id}@${e.symbol}@${e.bio.chainId}`).join(";")}#${r.bonds.map(e=>`${e.id}:${e.a1.id}-${e.a2.id}:${e.kind}`).join(";")}`,n=`${this._libCacheTag()}|${t??"d"}|${i}`,o=this._layoutCache.get(n);var r;if(void 0!==o)return this._layoutHits+=1,o;this._layoutMisses+=1;let s=void 0!==t?Ut(e,{bondLength:t}):Ut(e);return this._layoutCache.set(n,s),s}get stats(){return{parseHits:this._parseHits,parseMisses:this._parseMisses,layoutHits:this._layoutHits,layoutMisses:this._layoutMisses,renderHits:this._renderHits,renderMisses:this._renderMisses}}_libCacheTag(){let e=this.monomerLib,t="number"==typeof e.version?e.version:0;return`${this.monomerLib.source}@${t}`}},an=class{constructor(e,t){this.atoms=e,this.bonds=t,this.isEmpty=0===e.size&&0===t.size,Object.freeze(this)}},ln=new an(new Set,new Set),hn={empty:()=>ln,fromAtoms:e=>new an(new Set(e),new Set),fromBonds:e=>new an(new Set,new Set(e)),fromAtomsAndBonds:(e,t)=>new an(new Set(e),new Set(t)),union(...e){if(0===e.length)return ln;let t=new Set,i=new Set;for(let n of e){for(let e of n.atoms)t.add(e);for(let e of n.bonds)i.add(e)}return new an(t,i)},difference(e,t){let i=new Set,n=new Set;for(let n of e.atoms)t.atoms.has(n)||i.add(n);for(let i of e.bonds)t.bonds.has(i)||n.add(i);return new an(i,n)},intersect(e,t){let i=new Set,n=new Set;for(let n of e.atoms)t.atoms.has(n)&&i.add(n);for(let i of e.bonds)t.bonds.has(i)&&n.add(i);return new an(i,n)},toggle(e,t){if("atom"===t.kind){let i=new Set(e.atoms);return i.has(t.id)?i.delete(t.id):i.add(t.id),new an(i,new Set(e.bonds))}let i=new Set(e.bonds);return i.has(t.id)?i.delete(t.id):i.add(t.id),new an(new Set(e.atoms),i)},hasAtom:(e,t)=>e.atoms.has(t),hasBond:(e,t)=>e.bonds.has(t),equals(e,t){if(e===t)return!0;if(e.atoms.size!==t.atoms.size||e.bonds.size!==t.bonds.size)return!1;for(let i of e.atoms)if(!t.atoms.has(i))return!1;for(let i of e.bonds)if(!t.bonds.has(i))return!1;return!0}};function dn(e){let t=e.monomer;return null===t?0:t.rgroups.length}function cn(e,t){let i=dn(e);if(0===i)return[];let n=new Set(function(e,t){let i=new Set;for(let n of t)n.a1.id===e.id&&"numeric"===n.r1.kind&&i.add(n.r1.r),n.a2.id===e.id&&"numeric"===n.r2.kind&&i.add(n.r2.r);let n=[],o=Array.from(i).sort((e,t)=>e-t);for(let e of o)n.push(e);return n}(e,t)),o=[];for(let e=1;e<=i;e++)n.has(e)||o.push(e);return o}function un(e,t){let i=[];for(let n of t)if(n.a1.id===e.id){let e="numeric"===n.r1.kind?n.r1.r:0;i.push({bond:n,side:"r1",rNumber:e})}else if(n.a2.id===e.id){let e="numeric"===n.r2.kind?n.r2.r:0;i.push({bond:n,side:"r2",rNumber:e})}return i}function pn(e,t){return e.kind===t.kind&&("numeric"===e.kind&&"numeric"===t.kind?e.r===t.r:"positional"!==e.kind||"positional"!==t.kind||e.position===t.position&&e.r===t.r)}var mn=class{constructor(e){this._atoms=new Map,this._atomOrder=[],this._bonds=new Map,this._bondOrder=[],this._chains=new Map,this._chainOrder=[],this._addedAtoms=new Set,this._removedAtoms=new Set,this._modifiedAtoms=new Set,this._addedBonds=new Set,this._removedBonds=new Set,this._modifiedBonds=new Set,this._topologyDirty=!1,this._idgen=new oe;let t=function(e){let t=0;for(let i of e.atoms)i.id>t&&(t=i.id);for(let i of e.bonds)i.id>t&&(t=i.id);return t}(e);for(let e=0;e<t;e++)this._idgen.next();for(let t of e.chains)this._chains.set(t.id,{id:t.id,polymerType:t.polymerType,backboneAtomIds:t.backboneAtoms.map(e=>e.id),bondIds:t.bonds.map(e=>e.id),annotation:t.annotation}),this._chainOrder.push(t.id);for(let t of e.atoms)this._atoms.set(t.id,{id:t.id,p:{x:t.p.x,y:t.p.y},biotype:t.biotype,symbol:t.symbol,monomer:t.monomer,bio:{...t.bio},hidden:t.hidden,selected:t.selected,highlighted:t.highlighted,tag:t.tag,branchAtomId:t.branchAtom?.id,inlineSource:t.inlineSource}),this._atomOrder.push(t.id);for(let t of e.bonds)this._bonds.set(t.id,{id:t.id,a1Id:t.a1.id,a2Id:t.a2.id,kind:t.kind,r1:t.r1,r2:t.r2,ratio:t.ratio,tag:t.tag}),this._bondOrder.push(t.id);this._groups=[...e.groups],this._annotations=e.annotations}addAtom(e){let t=this._idgen.next(),i=function(e){switch(e){case X:return ne.PEPTIDE;case Q:case Z:case J:case ie:return ne.RNA;case ee:return ne.CHEM;case te:return ne.BLOB}}(e.biotype),n=e.chainId??this._pickChainId(i),o=this._chains.get(n);void 0===o&&(o={id:n,polymerType:i,backboneAtomIds:[],bondIds:[],annotation:void 0},this._chains.set(n,o),this._chainOrder.push(n));let r=e.positionInChain??o.backboneAtomIds.length+1,s={id:t,p:{x:e.p.x,y:e.p.y},biotype:e.biotype,symbol:e.symbol,monomer:null,bio:{chainId:n,positionInChain:r,continuousId:0},hidden:!1,selected:!1,highlighted:!1,tag:void 0,branchAtomId:void 0,inlineSource:void 0};this._atoms.set(t,s),this._atomOrder.push(t);let a=Math.max(0,Math.min(r-1,o.backboneAtomIds.length));return o.backboneAtomIds.splice(a,0,t),this._addedAtoms.add(t),this._topologyDirty=!0,t}removeAtom(e){let t=this._atoms.get(e);if(void 0===t)return;let i=[];for(let t of this._bonds.values())(t.a1Id===e||t.a2Id===e)&&i.push(t.id);for(let e of i)this._removeBondInternal(e);for(let t of this._atoms.values())t.branchAtomId===e&&(t.branchAtomId=void 0);let n=this._chains.get(t.bio.chainId);if(void 0!==n){let t=n.backboneAtomIds.indexOf(e);t>=0&&n.backboneAtomIds.splice(t,1)}this._atoms.delete(e);let o=this._atomOrder.indexOf(e);o>=0&&this._atomOrder.splice(o,1),this._addedAtoms.has(e)?this._addedAtoms.delete(e):this._removedAtoms.add(e),this._modifiedAtoms.delete(e),this._topologyDirty=!0}updateAtom(e,t){let i=this._atoms.get(e);void 0!==i&&(void 0!==t.p&&(i.p={x:t.p.x,y:t.p.y}),void 0!==t.symbol&&(i.symbol=t.symbol),void 0!==t.selected&&(i.selected=t.selected),void 0!==t.highlighted&&(i.highlighted=t.highlighted),"tag"in t&&(i.tag=t.tag),void 0!==t.hidden&&(i.hidden=t.hidden),this._addedAtoms.has(e)||this._modifiedAtoms.add(e))}addBond(e){if(!this._atoms.has(e.a1))throw new Error(`Transaction.addBond: atom ${e.a1} does not exist`);if(!this._atoms.has(e.a2))throw new Error(`Transaction.addBond: atom ${e.a2} does not exist`);for(let t of this._bonds.values()){let i=t.a1Id===e.a1&&t.a2Id===e.a2&&pn(t.r1,e.r1)&&pn(t.r2,e.r2),n=t.a1Id===e.a2&&t.a2Id===e.a1&&pn(t.r1,e.r2)&&pn(t.r2,e.r1);if(i||n)throw new Error(`Transaction.addBond: duplicate bond ${e.a1}:${fn(e.r1)}-${e.a2}:${fn(e.r2)}`)}let t=this._idgen.next();this._bonds.set(t,{id:t,a1Id:e.a1,a2Id:e.a2,kind:e.kind,r1:e.r1,r2:e.r2,ratio:void 0,tag:void 0}),this._bondOrder.push(t);let i=this._atoms.get(e.a1),n=this._atoms.get(e.a2);if(void 0!==i&&void 0!==n&&i.bio.chainId===n.bio.chainId){let e=this._chains.get(i.bio.chainId);void 0!==e&&e.bondIds.push(t)}return this._addedBonds.add(t),this._topologyDirty=!0,t}removeBond(e){this._bonds.has(e)&&(this._removeBondInternal(e),this._topologyDirty=!0)}updateBond(e,t){let i=this._bonds.get(e);void 0!==i&&("tag"in t&&(i.tag=t.tag),"ratio"in t&&(i.ratio=t.ratio),this._addedBonds.has(e)||this._modifiedBonds.add(e))}commit(){let e=new Map;for(let t of this._atomOrder){let i=this._atoms.get(t);if(void 0===i)continue;let n={id:i.id,p:{x:i.p.x,y:i.p.y},biotype:i.biotype,symbol:i.symbol,monomer:i.monomer,bio:{...i.bio},hidden:i.hidden,selected:i.selected,highlighted:i.highlighted,...void 0!==i.tag?{tag:i.tag}:{},...void 0!==i.inlineSource?{inlineSource:i.inlineSource}:{}};e.set(t,n)}for(let t of this._atomOrder){let i=this._atoms.get(t);if(void 0===i||void 0===i.branchAtomId)continue;let n=e.get(t),o=e.get(i.branchAtomId);void 0===n||void 0===o||(n.branchAtom=o)}let t=new Map;for(let i of this._bondOrder){let n=this._bonds.get(i);if(void 0===n)continue;let o=e.get(n.a1Id),r=e.get(n.a2Id);if(void 0===o||void 0===r)continue;let s={id:n.id,a1:o,a2:r,kind:n.kind,r1:n.r1,r2:n.r2,...void 0!==n.ratio?{ratio:{...n.ratio}}:{},...void 0!==n.tag?{tag:n.tag}:{}};t.set(i,s)}let i=[];for(let n of this._chainOrder){let o=this._chains.get(n);if(void 0===o||0===o.backboneAtomIds.length&&0===o.bondIds.length)continue;let r=[];for(let t of o.backboneAtomIds){let i=e.get(t);void 0!==i&&r.push(i)}let s=[];for(let e of o.bondIds){let i=t.get(e);void 0!==i&&s.push(i)}i.push({id:o.id,polymerType:o.polymerType,backboneAtoms:r,bonds:s,...void 0!==o.annotation?{annotation:o.annotation}:{}})}let n={atoms:this._atomOrder.map(t=>e.get(t)).filter(e=>void 0!==e),bonds:this._bondOrder.map(e=>t.get(e)).filter(e=>void 0!==e),chains:i,groups:[...this._groups],annotations:this._annotations};this._topologyDirty&&(n=function(e){let t=re(e),i=new Map;for(let n of e.atoms){let e=t.get(n.id);void 0!==e&&e!==n.bio.continuousId?i.set(n.id,{...n,bio:{...n.bio,continuousId:e}}):i.set(n.id,n)}for(let t of e.atoms){if(void 0===t.branchAtom)continue;let e=i.get(t.id),n=i.get(t.branchAtom.id);void 0===e||void 0===n||(e.branchAtom=n)}let n=e.bonds.map(e=>{let t=i.get(e.a1.id),n=i.get(e.a2.id);return void 0===t||void 0===n||t===e.a1&&n===e.a2?e:{...e,a1:t,a2:n}}),o=new Map;for(let e of n)o.set(e.id,e);let r=e.chains.map(e=>{let t=[];for(let n of e.backboneAtoms)t.push(i.get(n.id)??n);let n=[];for(let t of e.bonds)n.push(o.get(t.id)??t);return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:n,...void 0!==e.annotation?{annotation:e.annotation}:{}}});return{atoms:e.atoms.map(e=>i.get(e.id)??e),bonds:n,chains:r,groups:e.groups,annotations:e.annotations}}(n));let o=Object.freeze({addedAtomIds:new Set(this._addedAtoms),removedAtomIds:new Set(this._removedAtoms),addedBondIds:new Set(this._addedBonds),removedBondIds:new Set(this._removedBonds),modifiedAtomIds:new Set(this._modifiedAtoms),modifiedBondIds:new Set(this._modifiedBonds)});return this._addedAtoms.clear(),this._removedAtoms.clear(),this._modifiedAtoms.clear(),this._addedBonds.clear(),this._removedBonds.clear(),this._modifiedBonds.clear(),this._topologyDirty=!1,{mol:n,changes:o}}_removeBondInternal(e){if(void 0===this._bonds.get(e))return;this._bonds.delete(e);let t=this._bondOrder.indexOf(e);t>=0&&this._bondOrder.splice(t,1);for(let t of this._chains.values()){let i=t.bondIds.indexOf(e);i>=0&&t.bondIds.splice(i,1)}this._addedBonds.has(e)?this._addedBonds.delete(e):this._removedBonds.add(e),this._modifiedBonds.delete(e)}_pickChainId(e){let t=function(e){switch(e){case ne.PEPTIDE:return"PEPTIDE";case ne.RNA:return"RNA";case ne.CHEM:return"CHEM";case ne.BLOB:return"BLOB";case ne.G:return"G"}}(e),i=1;for(;this._chains.has(`${t}${i}`);)i+=1;return`${t}${i}`}};function fn(e){switch(e.kind){case"numeric":return`R${e.r}`;case"unspecified":return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${e.position}pos:R${e.r}`}}var bn=class{constructor(e,t,i){this.atoms=[],this.bonds=[],this.bondHitWidth=i?.bondHitWidth??4,this.rebuild(e,t)}rebuild(e,t){let i=[];for(let n of e.atoms)n.hidden||i.push({atom:n,bbox:ci(n,t),hitRadius:pi(n,t)});let n=[];for(let t of e.bonds)n.push({bond:t,a:t.a1.p,b:t.a2.p});this.atoms=i,this.bonds=n}test(e){let t=null,i=null;for(let n of this.atoms){if(!gn(e,n.bbox))continue;let o=e.x-n.atom.p.x,r=e.y-n.atom.p.y,s=Math.sqrt(o*o+r*r);s>n.hitRadius||(null===t||s<t.d?(i=t,t={entry:n,d:s}):(null===i||s<i.d)&&(i={entry:n,d:s}))}if(null!==t)return{atom:t.entry.atom};let n=null;for(let t of this.bonds){let i=An(e,t.a,t.b);i>this.bondHitWidth||(null===n||i<n.d)&&(n={entry:t,d:i})}return null!==n?{bond:n.entry.bond}:null}testRect(e){let t=[];for(let i of this.atoms)gn(i.atom.p,e)&&t.push(i.atom);let i=[];for(let t of this.bonds)gn(t.a,e)&&gn(t.b,e)&&i.push(t.bond);return{atoms:t,bonds:i}}atomCount(){return this.atoms.length}bondCount(){return this.bonds.length}};function gn(e,t){return e.x>=t.x&&e.x<=t.x+t.width&&e.y>=t.y&&e.y<=t.y+t.height}function An(e,t,i){let n=i.x-t.x,o=i.y-t.y,r=n*n+o*o;if(0===r){let i=e.x-t.x,n=e.y-t.y;return Math.sqrt(i*i+n*n)}let s=((e.x-t.x)*n+(e.y-t.y)*o)/r;s<0?s=0:s>1&&(s=1);let a=t.x+s*n,l=t.y+s*o,h=e.x-a,d=e.y-l;return Math.sqrt(h*h+d*d)}var _n=class{constructor(){this._handlers=new Map}on(e,t){let i=this._handlers.get(e);void 0===i&&(i=new Set,this._handlers.set(e,i));let n=t;return i.add(n),()=>{let t=this._handlers.get(e);void 0!==t&&t.delete(n)}}off(e,t){let i=this._handlers.get(e);void 0!==i&&i.delete(t)}fire(e,t){let i=this._handlers.get(e);if(void 0===i||0===i.size)return;let n=[...i];for(let e of n)e(t)}clear(){this._handlers.clear()}observerCount(e){if(void 0===e){let e=0;for(let t of this._handlers.values())e+=t.size;return e}return this._handlers.get(e)?.size??0}},yn=class{constructor(e){this._entries=[],this._idx=-1;let t=e?.maxEntries??100;if(t<=0)throw new RangeError("HistoryStack: maxEntries must be > 0");this._max=t}push(e){for(this._idx<this._entries.length-1&&(this._entries=this._entries.slice(0,this._idx+1)),this._entries.push(e),this._idx=this._entries.length-1;this._entries.length>this._max;)this._entries.shift(),this._idx-=1}canUndo(){return this._idx>0}canRedo(){return this._idx>=0&&this._idx<this._entries.length-1}undo(){return this.canUndo()?(this._idx-=1,this._entries[this._idx]??null):null}redo(){return this.canRedo()?(this._idx+=1,this._entries[this._idx]??null):null}clear(){this._entries=[],this._idx=-1}get size(){return this._entries.length}current(){return this._idx<0?null:this._entries[this._idx]??null}};function vn(e){let t=e.ownerDocument;if(null!=t)return t;let i=globalThis;if(void 0!==i.document)return i.document;throw new Error("EditorView: no Document available (host.ownerDocument is null).")}function wn(e,t,i,n){let o=e.createElement(t);if(void 0!==i)for(let e of Object.keys(i)){let t=i[e];!1===t||void 0===t||o.setAttribute(e,!0===t?"":String(t))}if(void 0!==n)for(let t of n)"string"==typeof t?o.appendChild(e.createTextNode(t)):o.appendChild(t);return o}function xn(e,t,i=220,n=140){if(null==e||""===t)return null;try{let o=e.get_mol(t);if(null===o)return null;let r=o.get_svg(i,n);return o.delete(),r}catch{return null}}function Cn(e,t,i){let n="data-testid";for(let i=0;i<e.body.children.length;i++){let o=e.body.children[i];if(void 0!==o&&o.getAttribute(n)===t)return o}let o=wn(e,"div",{class:i,[n]:t});return o.style.display="none",e.body.appendChild(o),o}function En(e,t,i){for(;null!==t.firstChild;)t.removeChild(t.firstChild);if(t.appendChild(wn(e,"div",{class:"hw-tooltip__symbol"},[i.symbol])),void 0!==i.name&&""!==i.name&&i.name!==i.symbol&&t.appendChild(wn(e,"div",{class:"hw-tooltip__name"},[i.name])),void 0!==i.rdkitSvg&&null!==i.rdkitSvg&&""!==i.rdkitSvg){let n={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(n["data-testid"]=i.rdkitTestid);let o=wn(e,"div",n);o.innerHTML=i.rdkitSvg,t.appendChild(o)}void 0!==i.hint&&""!==i.hint&&t.appendChild(wn(e,"div",{class:"hw-tooltip__hint"},[i.hint]))}function kn(e,t,i){let n=e.style;n.display="block",n.left=`${t+12}px`,n.top=`${i+12}px`}function Bn(e){null!==e&&(e.style.display="none")}function Sn(e){let t=e.body;if(null!=t)for(let e=0;e<t.children.length;e++){let i=t.children[e];if(void 0===i)continue;let n=void 0===i.getAttribute?null:i.getAttribute("data-testid");null!=n&&n.endsWith("-tooltip")&&Bn(i)}}var Mn=class e{constructor(e,t,i){this._baseTransform="",this._viewport={scale:1,offset:{x:0,y:0}},this._pinnedBbox=null,this._tooltip=null,this._bondTooltip=null,this._rdkitSvgCache=new Map,this._unsubs=[],this._destroyed=!1,this.host=e,this._editor=t,this._doc=i?.documentImpl??vn(e),this._width=i?.width??400,this._height=i?.height??200,function(e){let t=vn(e);if(null!==t.querySelector("style[data-hw-editor-view-styles]"))return;let i=t.createElement("style");i.setAttribute("data-hw-editor-view-styles",""),i.textContent=".hw-editor-view{position:relative;display:block;overflow:hidden;outline:none;}.hw-editor-view svg{display:block;user-select:none;}.hw-editor-view.hw-view-only{cursor:default;}";let n=t.head??t.documentElement;null!==n&&n.appendChild(i)}(e);let n=this._doc.createElement("div");n.setAttribute("class","hw-editor-view"),e.appendChild(n),this._tooltip=Cn(this._doc,"atom-tooltip","hw-atom-tooltip"),this._bondTooltip=Cn(this._doc,"bond-tooltip","hw-bond-tooltip"),this._svgRoot=this._renderFresh(),this._unsubs.push(t.on("mol:changed",e=>{this._hideTooltip(),this._hideBondTooltip(),("setHelm"===e.reason||"cleanLayout"===e.reason||"initial"===e.reason)&&(this._pinnedBbox=null),this._renderFresh()})),this._unsubs.push(t.on("selection:change",e=>{this._refreshOverlays(e)})),this._unsubs.push(t.on("highlight:change",e=>{this._refreshOverlays(e)})),this._unsubs.push(t.on("theme:change",()=>{this._renderFresh()})),this._unsubs.push(t.on("view:resize",e=>{this._applyResize(e.width,e.height)})),this._unsubs.push(t.on("view:viewport-change",e=>{this._viewport=e.viewport,this._applyViewport(e.viewport)})),this._unsubs.push(t.on("view:fit-to-content",()=>{this._pinnedBbox=null,this._renderFresh()})),this._unsubs.push(t.on("monomer:hover",e=>{this._showTooltip(e.atom,e.clientX,e.clientY)})),this._unsubs.push(t.on("monomer:hover-end",()=>{this._hideTooltip()})),this._unsubs.push(t.on("bond:hover",e=>{this._showBondTooltip(e.bond,e.clientX,e.clientY)})),this._unsubs.push(t.on("bond:hover-end",()=>{this._hideBondTooltip()})),this._unsubs.push(t.on("bond:preview",e=>{this._paintBondPreview(e.start.p,e.cursor,null!==e.candidate)})),this._unsubs.push(t.on("bond:preview-end",()=>{this._clearBondPreview()})),this._unsubs.push(t.on("bond:cancel",()=>{this._clearBondPreview()})),this._unsubs.push(t.on("selection:rectangle-start",e=>{this._paintSelectionRect(e.origin,e.origin)})),this._unsubs.push(t.on("selection:rectangle-update",e=>{this._paintSelectionRectFromRect(e.rect)})),this._unsubs.push(t.on("selection:rectangle-end",()=>{this._clearSelectionRect()}))}get svgRoot(){return this._svgRoot}get width(){return this._width}get height(){return this._height}resize(e,t){this._destroyed||(this._width=e,this._height=t,this._renderFresh())}redraw(){this._destroyed||this._renderFresh()}destroy(){if(this._destroyed)return;this._destroyed=!0;for(let e of this._unsubs)e();this._unsubs.length=0;let e=this.host.querySelector(".hw-editor-view");null!==e&&null!==e.parentNode&&e.parentNode.removeChild(e),Bn(this._tooltip),Bn(this._bondTooltip),this._tooltip=null,this._bondTooltip=null}_renderFresh(){let e=this._editor.getService(),t=this._currentTheme(),i=this._editor.getMol();null===this._pinnedBbox&&(this._pinnedBbox=xi(i,t));let n=e.renderMol(i,{width:this._width,height:this._height,theme:t,fixedModelBbox:this._pinnedBbox});this._svgRoot=function(e,t){let i=vn(e),n=e.querySelector(".hw-editor-view");if(null===n)throw new Error("EditorView.replaceSvg: missing .hw-editor-view wrapper.");let o=i.createElement("div");o.innerHTML=t;let r=o.querySelector("svg");if(null===r)throw new Error("EditorView.replaceSvg: rendered output contained no <svg>.");for(;null!==n.firstChild;)n.removeChild(n.firstChild);return n.appendChild(r),r}(this.host,n);let o=this._svgRoot.querySelector(".hw-content");return this._baseTransform=null!==o?o.getAttribute("transform")??"":"",this._svgRoot.setAttribute("data-testid","editor-svg"),this._applyOverlaysToCurrent(),(1!==this._viewport.scale||0!==this._viewport.offset.x||0!==this._viewport.offset.y)&&this._applyViewport(this._viewport),this._svgRoot}_refreshOverlays(e){this._applyOverlaysToCurrent()}_applyOverlaysToCurrent(){let e=this._editor.getMol(),t=this._editor.getSelection(),i=function(e,t={}){let i=t.theme??si,n=t.selectedAtomIds??new Set;return{highlightLayer:Ei(e,i,t.highlightedAtomIds??new Set),selectionLayer:ki(e,i,n)}}(e,{theme:this._currentTheme(),selectedAtomIds:t.atoms,highlightedAtomIds:this._editorHighlights()});this._spliceLayer("hw-highlights",i.highlightLayer),this._spliceLayer("hw-selections",i.selectionLayer)}_spliceLayer(e,t){let i=this._svgRoot.querySelector(`.${e}`);if(null===i||null===i.parentNode)return;let n=this._doc.createElementNS("http://www.w3.org/2000/svg","svg");n.innerHTML=t;let o=n.querySelector(`.${e}`);null!==o&&i.parentNode.replaceChild(o,i)}_editorHighlights(){let e=this._editor;return"function"==typeof e._currentHighlights?e._currentHighlights():new Set}_currentTheme(){let e=this._editor;return"function"==typeof e._currentTheme?e._currentTheme():this._editor.getService().theme}_applyResize(e,t){this._width=e,this._height=t,this._pinnedBbox=null,this._renderFresh()}_applyViewport(e){let t=this._svgRoot.querySelector(".hw-content");if(null===t)return;let i=`translate(${e.offset.x} ${e.offset.y}) scale(${e.scale})`,n=""===this._baseTransform?i:`${i} ${this._baseTransform}`;t.setAttribute("transform",n)}_showTooltip(e,t,i){let n=this._tooltip;if(null===n)return;let o=""===e.symbol?"?":e.symbol,r=e.monomer?.name??"",s=e.bio.positionInChain,a=""===e.bio.chainId?"?":e.bio.chainId,l=""!==r&&r!==o?`${r} @ ${a}:${s}`:`${o} @ ${a}:${s}`,h=this._renderRdkitTooltipSvg(e);En(this._doc,n,{symbol:o,name:l,rdkitSvg:h,rdkitTestid:"atom-tooltip-rdkit-svg"});let d=""!==r&&r!==o?`${o} — ${r} @ ${a}:${s}`:`${o} @ ${a}:${s}`,c=this._doc.createElement("div");c.setAttribute("class","hw-atom-tooltip__text"),c.style.display="none",c.appendChild(this._doc.createTextNode(d)),n.appendChild(c),kn(n,t,i)}_renderRdkitTooltipSvg(t){let i=this._editor.getService().options.rdkitModule;if(null==i)return null;let n=t.monomer;if(null===n)return null;let o=n.smiles;if(void 0===o||""===o)return null;let r=`${n.polymerType}:${n.symbol}`;if(this._rdkitSvgCache.has(r))return this._rdkitSvgCache.get(r)??null;let s=xn(i,o,220,140);if(this._rdkitSvgCache.size>=e._RDKIT_CACHE_LIMIT){let e=this._rdkitSvgCache.keys().next().value;void 0!==e&&this._rdkitSvgCache.delete(e)}return this._rdkitSvgCache.set(r,s),s}_hideTooltip(){Bn(this._tooltip)}_showBondTooltip(e,t,i){let n=this._bondTooltip;if(null===n)return;let o=In(e.r1),r=In(e.r2),s=`${e.a1.symbol}@${e.a1.bio.chainId}:${e.a1.bio.positionInChain}`,a=`${e.a2.symbol}@${e.a2.bio.chainId}:${e.a2.bio.positionInChain}`;En(this._doc,n,{symbol:`${o}-${r} (${e.kind})`,name:`${s} ↔ ${a}`}),kn(n,t,i)}_hideBondTooltip(){Bn(this._bondTooltip)}_paintBondPreview(e,t,i){let n=this._svgRoot.querySelector(".hw-content");if(null===n)return;let o=n.querySelector(".hw-bond-preview");null===o&&(o=this._doc.createElementNS("http://www.w3.org/2000/svg","line"),o.setAttribute("class","hw-bond-preview"),o.setAttribute("data-testid","bond-preview"),o.setAttribute("stroke-dasharray","6 4"),o.setAttribute("stroke-width","2"),o.setAttribute("fill","none"),o.setAttribute("pointer-events","none"),n.appendChild(o)),o.setAttribute("x1",String(e.x)),o.setAttribute("y1",String(e.y)),o.setAttribute("x2",String(t.x)),o.setAttribute("y2",String(t.y)),o.setAttribute("stroke",i?"#1f5fcd":"#999999")}_clearBondPreview(){let e=this._svgRoot.querySelector(".hw-bond-preview");null!==e&&null!==e.parentNode&&e.parentNode.removeChild(e)}_paintSelectionRect(e,t){let i=Math.min(e.x,t.x),n=Math.min(e.y,t.y),o=Math.abs(e.x-t.x),r=Math.abs(e.y-t.y);this._paintSelectionRectAt(i,n,o,r)}_paintSelectionRectFromRect(e){this._paintSelectionRectAt(e.x,e.y,e.width,e.height)}_paintSelectionRectAt(e,t,i,n){let o=this._svgRoot.querySelector(".hw-content");if(null===o)return;let r=o.querySelector(".hw-selection-rect");null===r&&(r=this._doc.createElementNS("http://www.w3.org/2000/svg","rect"),r.setAttribute("class","hw-selection-rect"),r.setAttribute("data-testid","selection-rect"),r.setAttribute("fill","rgba(31, 95, 205, 0.08)"),r.setAttribute("stroke","#1f5fcd"),r.setAttribute("stroke-width","1"),r.setAttribute("stroke-dasharray","4 3"),r.setAttribute("pointer-events","none"),o.appendChild(r)),r.setAttribute("x",String(e)),r.setAttribute("y",String(t)),r.setAttribute("width",String(i)),r.setAttribute("height",String(n))}_clearSelectionRect(){let e=this._svgRoot.querySelector(".hw-selection-rect");null!==e&&null!==e.parentNode&&e.parentNode.removeChild(e)}};Mn._RDKIT_CACHE_LIMIT=256;var Tn=Mn;function In(e){switch(e.kind){case"numeric":return`R${e.r}`;case"unspecified":return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${e.position}pos:R${e.r}`}}var Ln=class e{constructor(e,t){this._onClose=null,this._primaryAction=null,this._host=e,this._doc=t.documentImpl??vn(e);let i=this._doc,n={class:"hw-modal-backdrop",role:"presentation"};void 0!==t.testId&&(n["data-testid"]=`dialog-${t.testId}`);let o=wn(i,"div",n),r={class:"hw-modal",role:"dialog","aria-modal":"true","aria-label":t.title};void 0!==t.testId&&(r["data-testid"]=`dialog-${t.testId}-frame`);let s=wn(i,"div",r),a=wn(i,"div",{class:"hw-modal__header"},[t.title]),l=wn(i,"div",{class:"hw-modal__body"});s.appendChild(a),s.appendChild(l),o.appendChild(s);let h=e=>{e.stopPropagation()};for(let e of["mousedown","mousemove","mouseup","mouseover","mouseenter","mouseleave","wheel","contextmenu","dblclick","keydown","keyup","keypress"])o.addEventListener(e,h);s.addEventListener("keydown",e=>{let t=e;if("Enter"!==t.key||"TEXTAREA"===t.target?.tagName)return;let i=this._primaryAction;null!==i&&(t.preventDefault?.(),t.stopImmediatePropagation?.(),i())}),o.addEventListener("click",e=>{e.target!==o?e.stopPropagation():this.close()}),this.root=o,this.body=l}static anyOpen(){return e._openStack.length>0}static closeTopmost(){let t=e._openStack[e._openStack.length-1];return void 0!==t&&(t.close(),!0)}open(t){this._onClose=t??null,null===this.root.parentNode&&this._host.appendChild(this.root),e._openStack.includes(this)||e._openStack.push(this),Sn(this._doc)}close(){let t=e._openStack.indexOf(this);t>=0&&e._openStack.splice(t,1),null!==this.root.parentNode&&this.root.parentNode.removeChild(this.root);let i=this._onClose;this._onClose=null,null!==i&&i()}setPrimaryAction(e){this._primaryAction=e}get isOpen(){return null!==this.root.parentNode}};Ln._openStack=[];var $n=Ln;function Pn(e,t,i,n){let o=`hw-input-${Math.random().toString(36).slice(2,9)}`,r=wn(e,"label",{for:o,class:"hw-modal__label"},[t]),s=e.createElement("input");return s.setAttribute("id",o),s.setAttribute("type","text"),s.setAttribute("class","hw-modal__input"),void 0!==n&&s.setAttribute("data-testid",n),s.value=i,{row:wn(e,"div",{class:"hw-modal__row"},[r,s]),input:s}}function Rn(e,t,i,n,o){let r=`hw-sel-${Math.random().toString(36).slice(2,9)}`,s=wn(e,"label",{for:r,class:"hw-modal__label"},[t]),a=e.createElement("select");a.setAttribute("id",r),a.setAttribute("class","hw-modal__select"),void 0!==o&&a.setAttribute("data-testid",o);for(let t of i){let i=e.createElement("option");i.setAttribute("value",t.value),t.value===n&&i.setAttribute("selected",""),i.appendChild(e.createTextNode(t.label)),a.appendChild(i)}return{row:wn(e,"div",{class:"hw-modal__row"},[s,a]),select:a}}function Hn(e,t){let i=e.createElement("button");i.setAttribute("class","hw-modal__ok"),i.setAttribute("type","button"),void 0!==t&&i.setAttribute("data-testid",`${t}-ok`),i.appendChild(e.createTextNode("OK"));let n=e.createElement("button");return n.setAttribute("class","hw-modal__cancel"),n.setAttribute("type","button"),void 0!==t&&n.setAttribute("data-testid",`${t}-cancel`),n.appendChild(e.createTextNode("Cancel")),{row:wn(e,"div",{class:"hw-modal__actions"},[i,n]),ok:i,cancel:n}}var Nn=class{constructor(e,t){this._modal=null,this._editor=e;let i=e._getHost();if(null===i)throw new Error("ChooseRDialog: editor has no host element.");this._doc=t?.documentImpl??vn(i)}open(e,t,i){this.close();let n=this._editor._getHost();if(null===n)return Promise.resolve(null);let o=new $n(n,{documentImpl:this._doc,title:"Choose R-Groups",testId:"choose-r"});this._modal=o;let r=Fn(e,i?.freeR1,i?.currentR1,this._editor),s=Fn(t,i?.freeR2,i?.currentR2,this._editor),a=wn(this._doc,"div",{class:"hw-modal__info"},[`${e.symbol} (${e.bio.chainId})`]),l=void 0!==i?.currentR1?String(i.currentR1):r[0]?.value??"1",h=void 0!==i?.currentR2?String(i.currentR2):s[0]?.value??"1",d=Rn(this._doc,"R-group on side 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null!==this._modal&&this._modal.isOpen}close(){null!==this._modal&&(this._modal.close(),this._modal=null)}};function Dn(e){let t=e.value;if("string"==typeof t&&t.length>0){let e=Number(t);if(Number.isFinite(e)&&e>=1)return e}let i=e.querySelectorAll("option");for(let e of Array.from(i))if(null!==e.getAttribute("selected")){let t=e.getAttribute("value")??"",i=Number(t);if(Number.isFinite(i)&&i>=1)return i}let n=i[0];if(void 0!==n){let e=n.getAttribute("value")??"",t=Number(e);if(Number.isFinite(t)&&t>=1)return t}return 1}function Fn(e,t,i,n){let o,r=e.monomer?.rgroups;if(void 0===r||0===r.length)return[{value:"1",label:"R1"},{value:"2",label:"R2"},{value:"3",label:"R3"}];if(void 0!==t)o=new Set(t);else if(o=new Set(cn(e,n.getMol().bonds)),0===o.size)for(let e=1;e<=r.length;e++)o.add(e);void 0!==i&&i>=1&&i<=r.length&&o.add(i);let s=[],a=Array.from(o).sort((e,t)=>e-t);for(let e of a){let t=r[e-1];if(void 0===t)continue;let i=void 0!==t.capGroupName&&""!==t.capGroupName?` (${t.capGroupName})`:"";s.push({value:String(e),label:`${t.label}${i}`})}return s}var On="next-add-cursor";function zn(e){null!==e&&(e.style.display="none")}var Gn=class{constructor(e,t,i){this._hoverAtom=null,this._hoverBond=null,this._dragOrigin=null,this._bondStart=null,this._bondDragMoved=!1,this._rectDragHappened=!1,this._chooseRDialog=null,this._panStart=null,this._atomDragState=null,this._panMoved=!1,this._atomDragMoved=!1,this._nextAddCursorEl=null,this._destroyed=!1,this._unsubs=[],this._host=e,this._editor=t,this._enableContextMenu=i?.enableContextMenu??!0,this._tester=new bn(t.getMol(),t._currentTheme()),this._unsubs.push(t.on("mol:changed",()=>{this._tester=new bn(this._editor.getMol(),this._editor._currentTheme()),this._hoverAtom=null,this._hoverBond=null})),this._unsubs.push(t.on("option:change",e=>{("mode"===e.key||"nextAdd"===e.key)&&zn(this._nextAddCursorEl)})),this._onMove=e=>this._handleMove(e),this._onClick=e=>this._handleClick(e),this._onDblClick=e=>this._handleDblClick(e),this._onContextMenu=e=>this._handleContextMenu(e),this._onMouseDown=e=>this._handleMouseDown(e),this._onMouseUp=e=>this._handleMouseUp(e),this._onMouseLeave=e=>this._handleMouseLeave(e),this._onWheel=e=>this._handleWheel(e),e.addEventListener("mousemove",this._onMove),e.addEventListener("click",this._onClick),e.addEventListener("dblclick",this._onDblClick),e.addEventListener("contextmenu",this._onContextMenu),e.addEventListener("mousedown",this._onMouseDown),e.addEventListener("mouseup",this._onMouseUp),e.addEventListener("mouseleave",this._onMouseLeave),e.addEventListener("wheel",this._onWheel,{passive:!1})}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();this._host.removeEventListener("mousemove",this._onMove),this._host.removeEventListener("click",this._onClick),this._host.removeEventListener("dblclick",this._onDblClick),this._host.removeEventListener("contextmenu",this._onContextMenu),this._host.removeEventListener("mousedown",this._onMouseDown),this._host.removeEventListener("mouseup",this._onMouseUp),this._host.removeEventListener("mouseleave",this._onMouseLeave),this._host.removeEventListener("wheel",this._onWheel),null!==this._chooseRDialog&&(this._chooseRDialog.close(),this._chooseRDialog=null),zn(this._nextAddCursorEl),this._nextAddCursorEl=null}}_handleMove(e){if(null!==this._panStart){let t=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),i=t.x-this._panStart.origin.x,n=t.y-this._panStart.origin.y;return this._editor.panTo({x:this._panStart.initialOffset.x+i,y:this._panStart.initialOffset.y+n}),void(this._panMoved=!0)}if(null!==this._atomDragState){let t=this._toModel(e),i=t.x-this._atomDragState.pointerDownModel.x,n=t.y-this._atomDragState.pointerDownModel.y,o=[];for(let e of this._atomDragState.atomIds){let t=this._atomDragState.initialPositions.get(e);void 0!==t&&o.push({atomId:e,p:{x:t.x+i,y:t.y+n}})}return this._editor.moveAtoms(o),void(this._atomDragMoved=!0)}let t=this._toModel(e),i=this._tester.test(t),n=i?.atom??null,o=i?.bond??null;if(null!==this._bondStart){this._bondDragMoved=!0;let e=null!==n&&n.id!==this._bondStart.id?n:null;this._editor.fire("bond:preview",{start:this._bondStart,cursor:t,candidate:e,kind:"hbond"===this._editor.getMode()?"hbond":"backbone"})}if(null!==this._hoverAtom&&(null===n||n.id!==this._hoverAtom.id)&&(this._editor.fire("monomer:hover-end",{atom:this._hoverAtom}),this._hoverAtom=null),null!==n&&(null===this._hoverAtom||this._hoverAtom.id!==n.id)&&(this._hoverAtom=n,this._editor.fire("monomer:hover",{atom:n,clientX:e.clientX,clientY:e.clientY,modelX:t.x,modelY:t.y})),null!==this._hoverBond&&(null===o||o.id!==this._hoverBond.id)&&(this._editor.fire("bond:hover-end",{bond:this._hoverBond}),this._hoverBond=null),null!==o&&(null===this._hoverBond||this._hoverBond.id!==o.id)&&(this._hoverBond=o,this._editor.fire("bond:hover",{bond:o,clientX:e.clientX,clientY:e.clientY})),null!==this._dragOrigin){let e=Wn(this._dragOrigin,t);this._editor.fire("selection:rectangle-update",{rect:e})}this._updateNextAddCursor(e)}_handleClick(e){if(this._bondDragMoved)return void(this._bondDragMoved=!1);if(this._rectDragHappened)return void(this._rectDragHappened=!1);if(this._panMoved)return void(this._panMoved=!1);if(this._atomDragMoved)return void(this._atomDragMoved=!1);let t=this._toModel(e),i=this._tester.test(t),n=Yn(e),o=this._editor.getMode();if("eraser"===o)return void 0!==i?.atom?void this._editor.removeAtom(i.atom):void 0!==i?.bond?void this._editor.removeBond(i.bond):void 0;if(void 0===i?.atom)if(void 0===i?.bond){if(this._addsEnabled()){let e=this._editor.getNextAddSymbol();if(null!==e)return void this._editor.addAtom(t,e.biotype,e.symbol)}!n.shift&&!n.ctrl&&!n.meta&&this._editor.clearSelection()}else this._editor.fire("bond:click",{bond:i.bond,modifiers:n});else{if("select"===o&&!n.ctrl&&!n.shift&&!n.meta){let e=this._editor.getNextAddSymbol();if(null!==e)return i.atom.biotype===e.biotype?void this._editor.replaceMonomer(i.atom,e.symbol):void this._editor.fire("editor:status",{message:`Cannot replace: ${i.atom.biotype} is incompatible with ${e.biotype}`,severity:"warn",durationMs:3e3})}this._editor.fire("monomer:click",{atom:i.atom,modifiers:n,clientX:e.clientX,clientY:e.clientY})}}_handleDblClick(e){let t=this._toModel(e),i=this._tester.test(t),n=Yn(e);void 0===i?.atom?null===i&&this._editor.fitToContent():this._editor.fire("monomer:dblclick",{atom:i.atom,modifiers:n})}_handleContextMenu(e){this._enableContextMenu||e.preventDefault();let t=this._toModel(e),i=this._tester.test(t),n=()=>{e.preventDefault()};void 0!==i?.atom?this._editor.fire("monomer:contextmenu",{atom:i.atom,clientX:e.clientX,clientY:e.clientY,preventDefault:n}):void 0!==i?.bond&&this._editor.fire("bond:contextmenu",{bond:i.bond,clientX:e.clientX,clientY:e.clientY,preventDefault:n})}_handleMouseDown(e){if(0!==e.button)return;let t=this._toModel(e),i=this._tester.test(t),n=this._editor.getMode(),o=!0===e.ctrlKey||!0===e.metaKey,r=!0===e.shiftKey;if(void 0!==i?.atom){if("move"===n||"select"===n&&o){let e=this._editor.getSelection(),n=e.atoms.has(i.atom.id)?Array.from(e.atoms):[i.atom.id],o=this._editor.getMol(),r=new Map;for(let e of n){let t=o.atoms.find(t=>t.id===e);void 0!==t&&r.set(e,{x:t.p.x,y:t.p.y})}return this._atomDragState={atomIds:n,pointerDownModel:{x:t.x,y:t.y},initialPositions:r},void(this._atomDragMoved=!1)}return this._bondStart=i.atom,void(this._bondDragMoved=!1)}if(null===i){if("move"===n||"select"===n&&!r){let t=this._editor.getViewport();return this._panStart={origin:this._toViewBox({clientX:e.clientX,clientY:e.clientY}),initialOffset:{x:t.offset.x,y:t.offset.y}},void(this._panMoved=!1)}"select"===n&&r&&(this._dragOrigin=t,this._editor.fire("selection:rectangle-start",{origin:t}))}}_handleMouseUp(e){if(null!==this._panStart)return void(this._panStart=null);if(null!==this._atomDragState)return void(this._atomDragState=null);if(null!==this._bondStart){let t=this._bondStart,i=this._bondDragMoved;this._bondStart=null;let n=this._toModel(e),o=this._tester.test(n)?.atom;if(i&&void 0!==o&&o.id!==t.id){if(this._editor.fire("bond:preview-end",{start:t}),"hbond"===this._editor.getMode()){try{this._editor.addHydrogenBond(t,o)}catch{this._editor.fire("bond:cancel",{start:t})}return}let e=t.bio.chainId===o.bio.chainId&&Vn(t,o,this._editor.getMol())?"backbone":"cross-polymer",i=qn(t,o,this._editor.getMol().bonds,e);if("fail"===i.mode)return this._editor.fire("bond:cancel",{start:t}),void this._editor.fire("editor:status",{message:i.reason,severity:"error",durationMs:3e3});if("auto"===i.mode){try{this._editor.addBond(t,o,i.r1,i.r2,i.kind)}catch{this._editor.fire("bond:cancel",{start:t})}return}return void this._openChooseR(t,o,e,i.freeR1,i.freeR2)}if(i){let e=this._addsEnabled()?this._editor.getNextAddSymbol():null;if(null!==e){let i;try{i=this._editor.addAtom(n,e.biotype,e.symbol)}catch{return this._editor.fire("bond:cancel",{start:t}),void this._editor.fire("bond:preview-end",{start:t})}let o=this._editor.getMol().atoms.find(e=>e.id===t.id);if(void 0===o)return this._editor.fire("bond:cancel",{start:t}),void this._editor.fire("bond:preview-end",{start:t});let r=o.bio.chainId===i.bio.chainId&&Vn(o,i,this._editor.getMol())?"backbone":"cross-polymer",s=cn(o,this._editor.getMol().bonds),a=cn(i,this._editor.getMol().bonds);if(s.includes(2)&&a.includes(1)){try{this._editor.addBond(o,i,2,1,r)}catch{this._editor.fire("bond:cancel",{start:t})}return void this._editor.fire("bond:preview-end",{start:t})}let l=qn(o,i,this._editor.getMol().bonds,r);if("fail"===l.mode)return this._editor.fire("bond:cancel",{start:t}),this._editor.fire("editor:status",{message:l.reason,severity:"error",durationMs:3e3}),void this._editor.fire("bond:preview-end",{start:t});if("auto"===l.mode){try{this._editor.addBond(o,i,l.r1,l.r2,l.kind)}catch{this._editor.fire("bond:cancel",{start:t})}return void this._editor.fire("bond:preview-end",{start:t})}return this._editor.fire("bond:preview-end",{start:t}),void this._openChooseR(o,i,r,l.freeR1,l.freeR2)}return this._editor.fire("bond:cancel",{start:t}),void this._editor.fire("bond:preview-end",{start:t})}return}if(null===this._dragOrigin)return;let t=this._toModel(e),i=Wn(this._dragOrigin,t);this._dragOrigin=null;let n=this._tester.testRect(i),o=hn.fromAtomsAndBonds(n.atoms.map(e=>e.id),n.bonds.map(e=>e.id)),r=hn.union(this._editor.getSelection(),o);this._editor.setSelection(r),this._editor.fire("selection:rectangle-end",{rect:i,selection:r}),this._rectDragHappened=!0,r.atoms.size>0&&"select"===this._editor.getMode()&&this._editor.setMode("move")}_handleMouseLeave(e){null!==this._hoverAtom&&(this._editor.fire("monomer:hover-end",{atom:this._hoverAtom}),this._hoverAtom=null),null!==this._hoverBond&&(this._editor.fire("bond:hover-end",{bond:this._hoverBond}),this._hoverBond=null),null!==this._bondStart&&(this._editor.fire("bond:cancel",{start:this._bondStart}),this._editor.fire("bond:preview-end",{start:this._bondStart}),this._bondStart=null,this._bondDragMoved=!1),this._dragOrigin=null,this._panStart=null,this._atomDragState=null,this._panMoved=!1,this._atomDragMoved=!1,zn(this._nextAddCursorEl)}_openChooseR(e,t,i,n,o){null===this._chooseRDialog&&(this._chooseRDialog=new Nn(this._editor)),this._chooseRDialog.open(e,t,{freeR1:n,freeR2:o}).then(n=>{if(!this._destroyed){if(null===n)return void this._editor.fire("bond:cancel",{start:e});try{this._editor.addBond(e,t,n.r1,n.r2,i)}catch{this._editor.fire("bond:cancel",{start:e})}}})}_updateNextAddCursor(e){let t=this._editor.getNextAddSymbol(),i=this._editor.getMode(),n=null!==this._hoverAtom,o=null!==this._bondStart||null!==this._dragOrigin||null!==this._panStart||null!==this._atomDragState;if("select"!==i||null===t||n||o)return void(null!==this._nextAddCursorEl&&zn(this._nextAddCursorEl));let r=this._host.ownerDocument;if(null===r)return;null===this._nextAddCursorEl&&(this._nextAddCursorEl=function(e){let t="data-testid";for(let i=0;i<e.body.children.length;i++){let n=e.body.children[i];if(void 0!==n&&n.getAttribute(t)===On)return n}let i=e.createElement("div");return i.className="hw-next-add-cursor",i.setAttribute(t,On),i.style.display="none",e.body.appendChild(i),i}(r));let s=this._editor.getService().monomerLib,a=null;for(let e of s.getPolymerTypes()){let i=s.getMonomer(e,t.symbol);if(null!==i){a=i;break}}!function(e,t,i,n,o,r,s){let a=di({p:{x:0,y:0},biotype:i},o),l=Ie(n,i,o.colorTheme).background,h=_e(l),d=t.length,c=d<=1?1:Math.min(1,2/d),u=`<svg xmlns="http://www.w3.org/2000/svg" viewBox="-28 -28 56 56" width="56" height="56" class="hw-next-add-cursor__svg" aria-hidden="true"><path d="${a}" fill="${l}" stroke="${l}" stroke-width="5" stroke-linejoin="round" stroke-linecap="round"/><text x="0" y="0" text-anchor="middle" dominant-baseline="central" font-family="Helvetica Neue, Helvetica, Arial, sans-serif" font-size="${o.fontSize*c}" fill="${h}">${function(e){let t="";for(let i=0;i<e.length;i++){let n=e.charAt(i);t+="<"===n?"&lt;":">"===n?"&gt;":"&"===n?"&amp;":n}return t}(t)}</text></svg>`;e.innerHTML=u;let p=e.style;p.left=r-28+"px",p.top=s-28+"px",p.display="block"}(this._nextAddCursorEl,t.symbol,t.biotype,a,this._editor._currentTheme(),e.clientX,e.clientY)}_addsEnabled(){return"select"===this._editor.getMode()}_handleWheel(e){let t=!0===e.ctrlKey||!0===e.metaKey;if(e.preventDefault(),t)return void this._wheelPan(e);let i=e.deltaY<0?1.1:1/1.1,n=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),o=this._editor.getViewport(),r=0===o.scale?n:{x:(n.x-o.offset.x)/o.scale,y:(n.y-o.offset.y)/o.scale};this._editor.zoom(i,r)}_wheelPan(e){let t=e.deltaX??0,i=e.deltaY??0;if(0===t&&0===i)return;let n=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),o=this._toViewBox({clientX:e.clientX+t,clientY:e.clientY+i}),r=o.x-n.x,s=o.y-n.y,a=this._editor.getViewport();this._editor.panTo({x:a.offset.x-r,y:a.offset.y-s})}_toModel(e){let t=this._host.querySelector("svg"),i=null!==t?t.querySelector(".hw-content"):null;if(null!==t&&null!==i){let t=jn(i,e.clientX,e.clientY);if(null!==t)return t;let n=this._host.getBoundingClientRect(),o=e.clientX-n.left,r=e.clientY-n.top,s=function(e){if(""===e)return null;let t,i=0,n=0,o=1,r=/(translate|scale)\(([^)]+)\)/g,s=!1;for(;null!==(t=r.exec(e));){s=!0;let e=t[1],r=(t[2]??"").split(/[,\s]+/).map(e=>Number(e)).filter(e=>Number.isFinite(e));"translate"===e?(i+=o*(r[0]??0),n+=o*(r[1]??0)):"scale"===e&&(o*=r[0]??1)}return s?{tx:i,ty:n,scale:o}:null}(i.getAttribute("transform")??"");return null!==s?{x:(o-s.tx)/(0===s.scale?1:s.scale),y:(r-s.ty)/(0===s.scale?1:s.scale)}:{x:o,y:r}}let n=this._host.getBoundingClientRect();return{x:e.clientX-n.left,y:e.clientY-n.top}}_toViewBox(e){let t=this._host.querySelector("svg");if(null!==t){let i=jn(t,e.clientX,e.clientY);if(null!==i)return i;let n=this._host.getBoundingClientRect(),o=e.clientX-n.left,r=e.clientY-n.top,s=function(e){if(null===e||""===e)return null;let t=e.split(/[,\s]+/).map(e=>Number(e)).filter(e=>Number.isFinite(e));if(t.length<4)return null;let i=t[2],n=t[3];return i<=0||n<=0?null:{w:i,h:n}}(t.getAttribute("viewBox"));return null!==s&&n.width>0&&n.height>0?{x:o*(s.w/n.width),y:r*(s.h/n.height)}:{x:o,y:r}}let i=this._host.getBoundingClientRect();return{x:e.clientX-i.left,y:e.clientY-i.top}}};function qn(e,t,i,n){let o=dn(e),r=dn(t);if(0===o||0===r)return{mode:"auto",r1:2,r2:1,kind:n};let s=cn(e,i),a=cn(t,i);return 0===s.length?{mode:"fail",reason:`${e.symbol} has no free R-groups (max ${o}).`}:0===a.length?{mode:"fail",reason:`${t.symbol} has no free R-groups (max ${r}).`}:s.includes(2)&&a.includes(1)&&(1===s.length||1===a.length)?{mode:"auto",r1:2,r2:1,kind:n}:1===s.length&&1===a.length?{mode:"auto",r1:s[0],r2:a[0],kind:n}:{mode:"choose",freeR1:s,freeR2:a}}function jn(e,t,i){let n=e;if("function"!=typeof n.getScreenCTM)return null;let o=n.getScreenCTM();if(null===o)return null;let r=null;try{let e=o;"function"==typeof e.inverse&&(r=e.inverse())}catch{return null}if(null===r)return null;let s=n.ownerSVGElement;if(null!=s&&"function"==typeof s.createSVGPoint){let e=s.createSVGPoint();e.x=t,e.y=i;let n=e.matrixTransform(r);return{x:n.x,y:n.y}}let a=r;return{x:a.a*t+a.c*i+a.e,y:a.b*t+a.d*i+a.f}}function Vn(e,t,i){if(e.bio.chainId!==t.bio.chainId)return!1;let n=i.chains.find(t=>t.id===e.bio.chainId);if(void 0===n)return!1;let o=-1,r=-1;for(let i=0;i<n.backboneAtoms.length;i++){let s=n.backboneAtoms[i];s.id===e.id&&(o=i),s.id===t.id&&(r=i)}return!(o<0||r<0)&&1===Math.abs(o-r)}function Yn(e){return{shift:!0===e.shiftKey,alt:!0===e.altKey,ctrl:!0===e.ctrlKey,meta:!0===e.metaKey}}function Wn(e,t){return{x:Math.min(e.x,t.x),y:Math.min(e.y,t.y),width:Math.abs(e.x-t.x),height:Math.abs(e.y-t.y)}}var Un=class{constructor(e,t,i){this._destroyed=!1,this._host=e,this._editor=t,this._enabled=!1!==i?.enableKeyboard,this._enabled&&null===e.getAttribute("tabindex")&&e.setAttribute("tabindex","0"),this._onKey=e=>this._handleKey(e),e.addEventListener("keydown",this._onKey)}destroy(){this._destroyed||(this._destroyed=!0,this._host.removeEventListener("keydown",this._onKey))}_handleKey(e){if(!this._enabled)return;let t=this._classify(e),i={shift:!0===(n=e).shiftKey,alt:!0===n.altKey,ctrl:!0===n.ctrlKey,meta:!0===n.metaKey};var n;if(null===t)return void this._editor.fire("key:unhandled",{key:e.key,modifiers:i,preventDefault:()=>e.preventDefault()});let o=!1;this._editor.fire("key:command",{command:t,preventDefault:()=>{o=!0,e.preventDefault()}}),!o&&(e.preventDefault(),"clearSelection"!==t&&(e.stopPropagation(),e.stopImmediatePropagation?.()),this._execute(t))}_classify(e){let t=e.key,i=e.ctrlKey||e.metaKey;return"Delete"===t||"Backspace"===t?"delete":!i||"z"!==t&&"Z"!==t||e.shiftKey?i&&(("z"===t||"Z"===t)&&e.shiftKey||"y"===t||"Y"===t)?"redo":!i||"a"!==t&&"A"!==t?!i||"c"!==t&&"C"!==t?!i||"v"!==t&&"V"!==t?!i||"x"!==t&&"X"!==t?"Escape"===t?"clearSelection":"+"===t||"="===t?"zoomIn":"-"===t||"_"===t?"zoomOut":"0"===t?"fitToContent":"ArrowUp"===t?"nudgeUp":"ArrowDown"===t?"nudgeDown":"ArrowLeft"===t?"nudgeLeft":"ArrowRight"===t?"nudgeRight":null:"cut":"paste":"copy":"selectAll":"undo"}_execute(e){switch(e){case"delete":return void this._editor.deleteSelection();case"undo":return void this._editor.undo();case"redo":return void this._editor.redo();case"selectAll":return void this._editor.selectAll();case"clearSelection":return void this._editor.clearSelection();case"zoomIn":return void this._editor.zoom(1.1);case"zoomOut":return void this._editor.zoom(1/1.1);case"fitToContent":return void this._editor.fitToContent();case"nudgeUp":return void this._editor.nudgeSelection(0,-5);case"nudgeDown":return void this._editor.nudgeSelection(0,5);case"nudgeLeft":return void this._editor.nudgeSelection(-5,0);case"nudgeRight":return void this._editor.nudgeSelection(5,0);case"copy":{let e=this._editor.getHelm();return void this._editor.fire("clipboard:copy",{format:"helm",payload:e})}case"cut":{let e=this._editor.getHelm();return this._editor.fire("clipboard:copy",{format:"helm",payload:e}),void this._editor.deleteSelection()}case"paste":return void this._editor.fire("clipboard:paste",{format:"helm"});default:return}}},Kn=class{constructor(e,t){this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._destroyed=!1,this._unsubs=[],this._host=e,this._editor=t,this._tester=new bn(t.getMol(),t._currentTheme()),this._unsubs.push(t.on("mol:changed",()=>{this._tester=new bn(this._editor.getMol(),this._editor._currentTheme())})),this._onDragOver=e=>this._handleDragOver(e),this._onDrop=e=>this._handleDrop(e),this._onDragStart=e=>this._handleDragStart(e),this._onDragEnd=e=>this._handleDragEnd(e),this._onDragEnter=e=>this._handleDragEnter(e),this._onDragLeave=e=>this._handleDragLeave(e),e.addEventListener("dragover",this._onDragOver),e.addEventListener("drop",this._onDrop),e.addEventListener("dragstart",this._onDragStart),e.addEventListener("dragend",this._onDragEnd),e.addEventListener("dragenter",this._onDragEnter),e.addEventListener("dragleave",this._onDragLeave)}startPaletteDrag(e,t){this._currentPaletteSymbol=e,this._currentPaletteBiotype=t,this._editor.fire("dnd:start",{source:"palette",symbol:e})}cancelPaletteDrag(){null!==this._currentPaletteSymbol&&(this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._editor.fire("dnd:cancel",{source:"palette"}))}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();this._host.removeEventListener("dragover",this._onDragOver),this._host.removeEventListener("drop",this._onDrop),this._host.removeEventListener("dragstart",this._onDragStart),this._host.removeEventListener("dragend",this._onDragEnd),this._host.removeEventListener("dragenter",this._onDragEnter),this._host.removeEventListener("dragleave",this._onDragLeave)}}_activePaletteSymbol(e){if(null!==this._currentPaletteSymbol&&null!==this._currentPaletteBiotype)return{symbol:this._currentPaletteSymbol,biotype:this._currentPaletteBiotype};let t=e.dataTransfer;if(null==t)return null;try{let e="function"==typeof t.getData?t.getData("application/x-hwe-monomer"):"";if(""===e)return null;let i=JSON.parse(e);return"string"!=typeof i.symbol||"string"!=typeof i.biotype?null:{symbol:i.symbol,biotype:i.biotype}}catch{return null}}_handleDragEnter(e){if(null!==this._activePaletteSymbol(e)&&(e.preventDefault(),null!==e.dataTransfer&&void 0!==e.dataTransfer))try{e.dataTransfer.dropEffect="copy"}catch{}}_handleDragLeave(e){}_handleDragOver(e){if(null===this._activePaletteSymbol(e))return;if(e.preventDefault(),null!==e.dataTransfer&&void 0!==e.dataTransfer)try{e.dataTransfer.dropEffect="copy"}catch{}let t=this._toModel(e),i=this._tester.test(t),n=void 0!==i?.atom?i.atom:void 0!==i?.bond?i.bond:void 0,o={clientX:e.clientX,clientY:e.clientY};void 0!==n&&(o.target=n),this._editor.fire("dnd:over",o)}_handleDrop(e){let t=this._activePaletteSymbol(e);if(null===t)return;e.preventDefault();let{symbol:i,biotype:n}=t,o=this._toModel(e),r=this._tester.test(o),s=void 0!==r?.atom?r.atom:void 0!==r?.bond?r.bond:void 0,a={symbol:i,biotype:n,clientX:e.clientX,clientY:e.clientY};void 0!==s&&(a.target=s),this._editor.fire("dnd:drop",a),void 0!==r?.atom?this._editor.replaceMonomer(r.atom,i):this._editor.addAtom(o,n,i),this._currentPaletteSymbol=null,this._currentPaletteBiotype=null}_handleDragStart(e){this._editor.fire("dnd:start",{source:"canvas"})}_handleDragEnd(e){null!==this._currentPaletteSymbol&&(this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._editor.fire("dnd:cancel",{source:"palette"}))}_toModel(e){let t=this._host.querySelector("svg"),i=null!==t?t.querySelector(".hw-content"):null;if(null!==t&&null!==i){let t=function(e,t,i){let n=e;if("function"!=typeof n.getScreenCTM)return null;let o=n.getScreenCTM();if(null===o)return null;let r=null;try{let e=o;"function"==typeof e.inverse&&(r=e.inverse())}catch{return null}if(null===r)return null;let s=n.ownerSVGElement;if(null!=s&&"function"==typeof s.createSVGPoint){let e=s.createSVGPoint();e.x=t,e.y=i;let n=e.matrixTransform(r);return{x:n.x,y:n.y}}let a=r;return{x:a.a*t+a.c*i+a.e,y:a.b*t+a.d*i+a.f}}(i,e.clientX,e.clientY);if(null!==t)return t;let n=this._host.getBoundingClientRect(),o=e.clientX-n.left,r=e.clientY-n.top,s=function(e){if(""===e)return null;let t,i=0,n=0,o=1,r=/(translate|scale)\(([^)]+)\)/g,s=!1;for(;null!==(t=r.exec(e));){s=!0;let e=t[1],r=(t[2]??"").split(/[,\s]+/).map(e=>Number(e)).filter(e=>Number.isFinite(e));"translate"===e?(i+=o*(r[0]??0),n+=o*(r[1]??0)):"scale"===e&&(o*=r[0]??1)}return s?{tx:i,ty:n,scale:o}:null}(i.getAttribute("transform")??"");return null!==s?{x:(o-s.tx)/(0===s.scale?1:s.scale),y:(r-s.ty)/(0===s.scale?1:s.scale)}:{x:o,y:r}}let n=this._host.getBoundingClientRect();return{x:e.clientX-n.left,y:e.clientY-n.top}}},Xn=class{constructor(e,t){this._modal=null,this._atom=null,this._editor=e;let i=e._getHost();if(null===i)throw new Error("AtomPropsDialog: editor has no host element.");this._doc=t?.documentImpl??vn(i)}get isOpen(){return null!==this._modal&&this._modal.isOpen}open(e){this.close(),this._atom=e;let t=this._editor._getHost();if(null===t)return;let i=new $n(t,{documentImpl:this._doc,title:"Monomer Properties",testId:"atom-props"});this._modal=i;let n=wn(this._doc,"div",{class:"hw-modal__info"},[`Position ${e.bio.continuousId} in ${e.bio.chainId}`]),o=Pn(this._doc,"Symbol",e.symbol,"atom-props-symbol"),r=Pn(this._doc,"Annotation",e.bio.annotation??"","atom-props-annotation"),s=Hn(this._doc,"atom-props"),a=()=>this._commit(o.input.value,r.input.value);s.ok.addEventListener("click",a),s.cancel.addEventListener("click",()=>this.close()),i.setPrimaryAction(a),i.body.appendChild(n),i.body.appendChild(o.row),i.body.appendChild(r.row),i.body.appendChild(s.row),i.open()}close(){null!==this._modal&&(this._modal.close(),this._modal=null),this._atom=null}_commit(e,t){let i=this._atom;if(null===i)return void this.close();let n=e.trim(),o=(i.bio.annotation??"")!==t;if(n.length>0&&n!==i.symbol&&this._editor.replaceMonomer(i,n),o){let e=new mn(this._editor.getMol()),n={};n.tag=""===t?void 0:t,e.updateAtom(i.id,n);let{mol:o}=e.commit();this._editor.setMol(o);let r=o.atoms.find(e=>e.id===i.id);if(void 0!==r){let e={atom:r};void 0!==i.bio.annotation&&(e.oldAnnotation=i.bio.annotation),""!==t&&(e.newAnnotation=t),this._editor.fire("monomer:annotate",e)}}this.close()}},Qn=class{constructor(e,t){this._modal=null,this._bond=null,this._editor=e;let i=e._getHost();if(null===i)throw new Error("BondPropsDialog: editor has no host element.");this._doc=t?.documentImpl??vn(i)}get isOpen(){return null!==this._modal&&this._modal.isOpen}open(e){this.close(),this._bond=e;let t=this._editor._getHost();if(null===t)return;let i=new $n(t,{documentImpl:this._doc,title:"Bond Properties",testId:"bond-props"});this._modal=i;let n=wn(this._doc,"div",{class:"hw-modal__info"},[`Kind: ${e.kind}`]),o=this._buildAtomsPreviewRow(e),r="numeric"===e.r1.kind,s="numeric"===e.r2.kind,a=r&&s,l=this._editor.getMol().bonds,h=a?Zn(e.r1,e.a1,l):[],d=a?Zn(e.r2,e.a2,l):[],c=null,u=null;if(a){let t=String(e.r1.r),i=String(e.r2.r);c=Rn(this._doc,`R-group on ${e.a1.symbol} (${e.a1.bio.chainId}:${e.a1.bio.positionInChain})`,h,t,"bond-props-r1"),u=Rn(this._doc,`R-group on ${e.a2.symbol} (${e.a2.bio.chainId}:${e.a2.bio.positionInChain})`,d,i,"bond-props-r2")}let p=Hn(this._doc,"bond-props"),m=()=>{let t=null!==c?Number(Jn(c.select,e.r1.r)):null,i=null!==u?Number(Jn(u.select,e.r2.r)):null;this._commit(t,i)};p.ok.addEventListener("click",m),p.cancel.addEventListener("click",()=>this.close()),i.setPrimaryAction(m),i.body.appendChild(n),null!==o&&i.body.appendChild(o),null!==c&&i.body.appendChild(c.row),null!==u&&i.body.appendChild(u.row),i.body.appendChild(p.row),i.open()}_buildAtomsPreviewRow(e){let t=this._rdkit(),i=this._buildAtomCell(e.a1,t,"bond-props-atom-a1"),n=this._buildAtomCell(e.a2,t,"bond-props-atom-a2"),o=wn(this._doc,"div",{class:"hw-bond-props__bond-arrow"},["↔"]);return wn(this._doc,"div",{class:"hw-bond-props__atoms","data-testid":"bond-props-atoms"},[i,o,n])}_buildAtomCell(e,t,i){let n=e.monomer?.name??e.symbol,o=e.symbol===n?e.symbol:`${e.symbol} — ${n}`,r=wn(this._doc,"div",{class:"hw-bond-props__atom-label"},[o]),s={class:"hw-bond-props__atom-rdkit","data-testid":`${i}-rdkit`},a=wn(this._doc,"div",s),l=e.monomer?.smiles;if(null!==t&&void 0!==l&&""!==l){let e=xn(t,l,220,140);null!==e&&""!==e&&(a.innerHTML=e)}return wn(this._doc,"div",{class:"hw-bond-props__atom","data-testid":i},[r,a])}_rdkit(){let e=this._editor.getService().options?.rdkitModule;return e??null}close(){null!==this._modal&&(this._modal.close(),this._modal=null),this._bond=null}_commit(e,t){let i=this._bond;if(null===i)return void this.close();let n="numeric"===i.r1.kind?i.r1.r:null,o="numeric"===i.r2.kind?i.r2.r:null;if(null===e||null===t||e===n&&t===o)this.close();else{if(null!==e&&null!==t){let r=i.kind,s=i.a1,a=i.a2;this._editor.removeBond(i);try{this._editor.addBond(s,a,e,t,r)}catch(e){if(null!==n&&null!==o)try{this._editor.addBond(s,a,n,o,i.kind)}catch{}}}this.close()}}};function Zn(e,t,i){let n=t.monomer?.rgroups;if(void 0===n||0===n.length)return[{value:"1",label:"R1"},{value:"2",label:"R2"},{value:"3",label:"R3"}];let o=new Set(cn(t,i));o.add(e.r);let r=Array.from(o).sort((e,t)=>e-t),s=[];for(let e of r){let t=n[e-1];if(void 0===t)continue;let i=void 0!==t.capGroupName&&""!==t.capGroupName?` (${t.capGroupName})`:"";s.push({value:String(e),label:`${t.label}${i}`})}return s}function Jn(e,t){let i=e.value;if("string"==typeof i&&i.length>0){let e=Number(i);if(Number.isFinite(e)&&e>=1)return e}let n=e.querySelectorAll("option");for(let e of Array.from(n))if(null!==e.getAttribute("selected")){let t=e.getAttribute("value")??"",i=Number(t);if(Number.isFinite(i)&&i>=1)return i}return t}var eo=class{constructor(e,t){this._modal=null,this._result=null,this._findInput=null,this._replaceInput=null,this._matches=[],this._cursor=-1,this._editor=e;let i=e._getHost();if(null===i)throw new Error("FindReplaceDialog: editor has no host element.");this._doc=t?.documentImpl??vn(i)}get isOpen(){return null!==this._modal&&this._modal.isOpen}open(){this.close();let e=this._editor._getHost();if(null===e)return;let t=new $n(e,{documentImpl:this._doc,title:"Find / Replace",testId:"find-replace"});this._modal=t;let i=Pn(this._doc,"Find","","find-replace-find"),n=Pn(this._doc,"Replace with","","find-replace-replace");this._findInput=i.input,this._replaceInput=n.input;let o=this._doc.createElement("button");o.setAttribute("class","hw-modal__find-next"),o.setAttribute("type","button"),o.setAttribute("data-testid","find-replace-next"),o.appendChild(this._doc.createTextNode("Find Next")),o.addEventListener("click",()=>this._findNext());let r=this._doc.createElement("button");r.setAttribute("class","hw-modal__replace"),r.setAttribute("type","button"),r.setAttribute("data-testid","find-replace-replace-one"),r.appendChild(this._doc.createTextNode("Replace")),r.addEventListener("click",()=>this._replaceOne());let s=this._doc.createElement("button");s.setAttribute("class","hw-modal__replace-all"),s.setAttribute("type","button"),s.setAttribute("data-testid","find-replace-replace-all"),s.appendChild(this._doc.createTextNode("Replace All")),s.addEventListener("click",()=>this._replaceAll());let a=this._doc.createElement("button");a.setAttribute("class","hw-modal__cancel"),a.setAttribute("type","button"),a.setAttribute("data-testid","find-replace-close"),a.appendChild(this._doc.createTextNode("Close")),a.addEventListener("click",()=>this.close());let l=wn(this._doc,"div",{class:"hw-modal__actions"},[o,r,s,a]),h=wn(this._doc,"div",{class:"hw-modal__result","data-testid":"find-replace-result"},["0 matches"]);this._result=h,t.setPrimaryAction(()=>this._findNext()),t.body.appendChild(i.row),t.body.appendChild(n.row),t.body.appendChild(l),t.body.appendChild(h),t.open()}close(){null!==this._modal&&(this._modal.close(),this._modal=null),this._result=null,this._findInput=null,this._replaceInput=null,this._matches=[],this._cursor=-1}_findNext(){let e=this._findInput?.value.trim()??"";if(""===e)return void this._setResultText("Enter a symbol to find");let t=this._editor.findMonomers(e);if(this._matches=t.map(e=>e.id),0===this._matches.length)return this._cursor=-1,this._editor.setHighlights([]),void this._setResultText("No matches");this._cursor=(this._cursor+1)%this._matches.length;let i=this._matches[this._cursor];void 0!==i&&this._editor.setHighlights([i]),this._setResultText(`${this._cursor+1} / ${this._matches.length} matches`)}_replaceOne(){let e=this._findInput?.value.trim()??"",t=this._replaceInput?.value.trim()??"";if(""===e||""===t)return void this._setResultText("Both Find and Replace fields are required");if(0===this._matches.length||this._cursor<0)return void this._findNext();let i=this._matches[this._cursor];if(void 0===i)return;let n=this._editor.getMol().atoms.find(e=>e.id===i);if(void 0!==n)if(this._editor.replaceMonomer(n,t),this._matches.splice(this._cursor,1),0===this._matches.length)this._cursor=-1,this._editor.setHighlights([]),this._setResultText("Replaced; no further matches");else{this._cursor=this._cursor%this._matches.length;let e=this._matches[this._cursor];void 0!==e&&this._editor.setHighlights([e]),this._setResultText(`${this._matches.length} matches remaining`)}}_replaceAll(){let e=this._findInput?.value.trim()??"",t=this._replaceInput?.value.trim()??"";if(""===e||""===t)return void this._setResultText("Both Find and Replace fields are required");let i=this._editor.replaceMonomers(e,t);this._matches=[],this._cursor=-1,this._editor.setHighlights([]),this._setResultText(`${i} replacement${1===i?"":"s"} made`)}_setResultText(e){if(null!==this._result){for(;null!==this._result.firstChild;)this._result.removeChild(this._result.firstChild);this._result.appendChild(this._doc.createTextNode(e))}}},to=Object.freeze(new Set),io=class{constructor(e,t){if(this._events=new _n,this._destroyed=!1,this._view=null,this._pointer=null,this._keyboard=null,this._dnd=null,this._atomDialog=null,this._bondDialog=null,this._findReplaceDialog=null,this._viewBootstrapped=!1,this._mode="select",this._nextAdd=null,this._lastAction=null,this._lastTripletSugarPos=null,void 0===t.service||null===t.service)throw new TypeError("HelmEditor: options.service is required");this._host=e,this._service=t.service,this._options=Object.freeze({...t}),this._mol=Y(),this._selection=hn.empty(),this._highlights=to,this._theme=t.service.theme??si,this._viewport={scale:1,offset:{x:0,y:0}},this._viewOnly=t.viewOnly??!1,this._history=new yn({maxEntries:100}),this._history.push({mol:this._mol,label:"initial"}),this._libUnsub=this._service.monomerLib.onChanged.subscribe(e=>{let t=this._service.monomerLib,i="number"==typeof t.version?t.version:0,n="reload"===e.type?"replace":"update";this._events.fire("monomer-lib:change",{source:this._service.monomerLib.source,version:i,reason:n})}),void 0!==t.initialHelm&&this.setHelm(t.initialHelm),this._bootstrapWaveB()}_bootstrapWaveB(){if(this._viewBootstrapped||null===this._host)return;let e=this._resolveDocument(this._host);if(null===e)return;this._viewBootstrapped=!0;let t={documentImpl:e};void 0!==this._options.width&&(t.width=this._options.width),void 0!==this._options.height&&(t.height=this._options.height),this._view=new Tn(this._host,this,t),!0!==this._viewOnly&&(this._pointer=new Gn(this._host,this,{enableContextMenu:this._options.enableContextMenu??!0})),!1!==this._options.enableKeyboard&&(this._keyboard=new Un(this._host,this,{enableKeyboard:!0})),!1!==this._options.enableDragDrop&&(this._dnd=new Kn(this._host,this)),this._events.on("monomer:hover",e=>{this.setHighlights([e.atom.id])}),this._events.on("monomer:hover-end",()=>{this.clearHighlights()}),this._events.on("monomer:click",e=>{let t=e.modifiers;!0!==t.ctrl&&!0!==t.meta?!0!==t.shift?this.setSelection(hn.fromAtoms([e.atom.id])):this.setSelection(hn.union(this._selection,hn.fromAtoms([e.atom.id]))):this.setSelection(hn.toggle(this._selection,{kind:"atom",id:e.atom.id}))})}_resolveDocument(e){let t=e.ownerDocument;if(null!=t)return t;let i=globalThis;return void 0!==i.document?i.document:null}destroy(){this._destroyed||(this._destroyed=!0,null!==this._atomDialog&&(this._atomDialog.close(),this._atomDialog=null),null!==this._bondDialog&&(this._bondDialog.close(),this._bondDialog=null),null!==this._findReplaceDialog&&(this._findReplaceDialog.close(),this._findReplaceDialog=null),null!==this._dnd&&(this._dnd.destroy(),this._dnd=null),null!==this._keyboard&&(this._keyboard.destroy(),this._keyboard=null),null!==this._pointer&&(this._pointer.destroy(),this._pointer=null),null!==this._view&&(this._view.destroy(),this._view=null),this._libUnsub(),this._events.clear(),this._history.clear())}resize(e,t){this._ensureLive(),null!==this._view&&this._view.resize(e,t),this._events.fire("view:resize",{width:e,height:t})}redraw(){this._ensureLive(),null===this._view?this._events.fire("render:skip",{reason:"no-view-mounted"}):this._view.redraw()}setHelm(e,t){this._ensureLive();let i=t?.canonicalize??this._options.canonicalize??!1,n=this._service.parse(e,{mode:"lenient"}),o=n.diagnostics;o.filter(e=>"error"===e.severity).length>0&&this._events.fire("helm:parse-error",{helm:e,diagnostics:o});for(let e of o)"error"===e.severity?this._events.fire("validation:error",{diagnostic:e}):"warning"===e.severity&&this._events.fire("validation:warning",{diagnostic:e});let r=n.mol;if(i){let t=this._service.canonicalize(e);r=this._service.parse(t,{mode:"lenient"}).mol}let s=Ut(r,void 0!==this._options.bondLength?{bondLength:this._options.bondLength}:void 0);return this._replaceMol(s,"setHelm","api"),{mol:s,diagnostics:o}}getHelm(e){this._ensureLive();let t={};return void 0!==e?.canonicalize&&(t.canonicalize=e.canonicalize),void 0!==e?.includeHighlights&&(t.includeHighlights=e.includeHighlights),this._service.serialize(this._mol,t)}setMol(e){this._ensureLive(),this._replaceMol(e,"setMol","api")}getMol(){return this._mol}getService(){return this._service}getSelection(){return this._selection}setSelection(e){if(this._ensureLive(),hn.equals(this._selection,e))return;let t=hn.difference(e,this._selection),i=hn.difference(this._selection,e);this._selection=e,this._events.fire("selection:change",{selection:e,addedAtomIds:t.atoms,removedAtomIds:i.atoms,addedBondIds:t.bonds,removedBondIds:i.bonds})}selectAll(){this._ensureLive();let e=this._mol.atoms.map(e=>e.id),t=this._mol.bonds.map(e=>e.id);this.setSelection(hn.fromAtomsAndBonds(e,t))}clearSelection(){this._ensureLive(),!this._selection.isEmpty&&this.setSelection(hn.empty())}setHighlights(e){this._ensureLive();let t=new Set(e);this._highlights=t,this._events.fire("highlight:change",{atomIds:t,bondIds:to})}clearHighlights(){this._ensureLive(),0!==this._highlights.size&&(this._highlights=to,this._events.fire("highlight:change",{atomIds:to,bondIds:to}))}addAtom(e,t,i){this._ensureLive();let n=new mn(this._mol),o=n.addAtom({p:e,biotype:t,symbol:i}),{mol:r}=n.commit(),s=Pe(r,this._service.monomerLib,{mode:"lenient"}).mol;this._replaceMol(s,`addAtom:${i}`,"api");let a=W(s,o);if(void 0===a)throw new Error("HelmEditor.addAtom: lost atom after commit");return this._events.fire("monomer:add",{atom:a,source:"api"}),a}removeAtom(e){this._ensureLive();let t="number"==typeof e?e:e.id,i=W(this._mol,t);if(void 0===i)return;let n=new mn(this._mol);n.removeAtom(t);let{mol:o}=n.commit();this._replaceMol(o,`removeAtom:${i.symbol}`,"api"),this._events.fire("monomer:remove",{atom:i,source:"api"})}addBond(e,t,i,n,o){let r,s;this._ensureLive();try{this._validateAddBondConstraints(e,t,i,n);let a=o??"backbone",l=this._maybeMergeForLinearExtend(e,t,i,n,a);if(null!==l)({id:r,mol:s}=l);else{let a=new mn(this._mol);r=a.addBond({a1:e.id,a2:t.id,kind:o??"backbone",r1:{kind:"numeric",r:i},r2:{kind:"numeric",r:n}}),({mol:s}=a.commit())}}catch(o){let r=o instanceof P?o.message:this._friendlyBondError(o instanceof Error?o.message:String(o),e,t,i,n);throw this._events.fire("editor:status",{message:`Could not add bond: ${r}`,severity:"error",durationMs:3e3}),o}this._replaceMol(s,"addBond","api");let a=U(s,r);if(void 0===a)throw new Error("HelmEditor.addBond: lost bond after commit");return this._events.fire("bond:add",{bond:a,source:"api"}),a}_maybeMergeForLinearExtend(e,t,i,n,o){if(e.bio.chainId===t.bio.chainId||"backbone"!==o&&"cross-polymer"!==o)return null;let r=this._mol.chains.find(t=>t.id===e.bio.chainId),s=this._mol.chains.find(e=>e.id===t.bio.chainId);if(void 0===r||void 0===s||r.polymerType!==s.polymerType||r.polymerType===ne.CHEM||r.polymerType===ne.BLOB)return null;if(2===i&&1===n){let i=r.backboneAtoms[r.backboneAtoms.length-1],n=s.backboneAtoms[0];if(void 0!==i&&void 0!==n&&i.id===e.id&&n.id===t.id)return this._mergeChains(r,s,o)}if(1===i&&2===n){let i=r.backboneAtoms[0],n=s.backboneAtoms[s.backboneAtoms.length-1];if(void 0!==i&&void 0!==n&&i.id===e.id&&n.id===t.id)return this._mergeChains(s,r,o)}return null}_mergeChains(e,t,i){let n=e.backboneAtoms.length,o=new Set;for(let e of t.backboneAtoms)o.add(e.id),void 0!==e.branchAtom&&o.add(e.branchAtom.id);let r=new Map,s=n;for(let i of t.backboneAtoms){s+=1;let t={...i,bio:{...i.bio,chainId:e.id,positionInChain:s}};if(r.set(i.id,t),void 0!==i.branchAtom){let t=i.branchAtom,n={...t,bio:{...t.bio,chainId:e.id,positionInChain:s}};r.set(t.id,n)}}for(let e of t.backboneAtoms){let t=r.get(e.id);if(void 0===t||void 0===e.branchAtom)continue;let i=r.get(e.branchAtom.id);void 0!==i&&(t.branchAtom=i)}for(let e of this._mol.atoms)r.has(e.id)||r.set(e.id,e);let a=0;for(let e of this._mol.atoms)e.id>a&&(a=e.id);for(let e of this._mol.bonds)e.id>a&&(a=e.id);let l=a+1,h={id:l,a1:r.get(e.backboneAtoms[e.backboneAtoms.length-1].id),a2:r.get(t.backboneAtoms[0].id),kind:"backbone",r1:{kind:"numeric",r:2},r2:{kind:"numeric",r:1}},d=[];for(let e of this._mol.bonds){let t=r.get(e.a1.id)??e.a1,i=r.get(e.a2.id)??e.a2;t===e.a1&&i===e.a2?d.push(e):d.push({...e,a1:t,a2:i})}d.push(h);let c=[],u=[...e.backboneAtoms];for(let e of t.backboneAtoms)u.push(r.get(e.id));for(let i of this._mol.chains)if(i.id!==t.id)if(i.id===e.id){let e=i.bonds.map(e=>{let t=r.get(e.a1.id)??e.a1,i=r.get(e.a2.id)??e.a2;return t===e.a1&&i===e.a2?e:{...e,a1:t,a2:i}});for(let i of t.bonds){let t=r.get(i.a1.id)??i.a1,n=r.get(i.a2.id)??i.a2;e.push(t===i.a1&&n===i.a2?i:{...i,a1:t,a2:n})}e.push(h),c.push({id:i.id,polymerType:i.polymerType,backboneAtoms:u,bonds:e,...void 0!==i.annotation?{annotation:i.annotation}:{}})}else{let e=i.backboneAtoms.map(e=>r.get(e.id)??e),t=i.bonds.map(e=>{let t=r.get(e.a1.id)??e.a1,i=r.get(e.a2.id)??e.a2;return t===e.a1&&i===e.a2?e:{...e,a1:t,a2:i}});c.push({id:i.id,polymerType:i.polymerType,backboneAtoms:e,bonds:t,...void 0!==i.annotation?{annotation:i.annotation}:{}})}let p={atoms:this._mol.atoms.map(e=>r.get(e.id)??e),bonds:d,chains:c,groups:this._mol.groups,annotations:this._mol.annotations};return p=this._refreshContinuousIdsLocal(p),{id:l,mol:p}}_refreshContinuousIdsLocal(e){let t=re(e),i=new Map;for(let n of e.atoms){let e=t.get(n.id);void 0!==e&&e!==n.bio.continuousId?i.set(n.id,{...n,bio:{...n.bio,continuousId:e}}):i.set(n.id,n)}for(let t of e.atoms){if(void 0===t.branchAtom)continue;let e=i.get(t.id),n=i.get(t.branchAtom.id);void 0===e||void 0===n||(e.branchAtom=n)}let n=e.bonds.map(e=>{let t=i.get(e.a1.id)??e.a1,n=i.get(e.a2.id)??e.a2;return t===e.a1&&n===e.a2?e:{...e,a1:t,a2:n}}),o=new Map;for(let e of n)o.set(e.id,e);let r=e.chains.map(e=>{let t=e.backboneAtoms.map(e=>i.get(e.id)??e),n=e.bonds.map(e=>o.get(e.id)??e);return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:n,...void 0!==e.annotation?{annotation:e.annotation}:{}}});return{atoms:e.atoms.map(e=>i.get(e.id)??e),bonds:n,chains:r,groups:e.groups,annotations:e.annotations}}_friendlyBondError(e,t,i,n,o){return e.includes("duplicate bond")?`bond ${t.symbol}:R${n} ↔ ${i.symbol}:R${o} already exists`:e.includes("does not exist")?"one of the endpoint atoms is missing":e}_validateAddBondConstraints(e,t,i,n){let o=this._mol.bonds,r=dn(e);if(r>0&&(i<1||i>r))throw new P("rgroup-not-on-monomer",`R-group R${i} is not defined on monomer '${e.symbol}' (has R1..R${r})`,{atomId:e.id,requested:i,total:r});let s=dn(t);if(s>0&&(n<1||n>s))throw new P("rgroup-not-on-monomer",`R-group R${n} is not defined on monomer '${t.symbol}' (has R1..R${s})`,{atomId:t.id,requested:n,total:s});if(r>0){let t=un(e,o).find(e=>e.rNumber===i);if(void 0!==t){let n="r1"===t.side?t.bond.a2:t.bond.a1;throw new P("rgroup-already-bonded",`R-group R${i} on '${e.symbol}' is already bonded to '${n.symbol}' (${n.bio.chainId}:${n.bio.positionInChain})`,{atomId:e.id,requested:i,conflictingBondId:t.bond.id})}}if(s>0){let e=un(t,o).find(e=>e.rNumber===n);if(void 0!==e){let i="r1"===e.side?e.bond.a2:e.bond.a1;throw new P("rgroup-already-bonded",`R-group R${n} on '${t.symbol}' is already bonded to '${i.symbol}' (${i.bio.chainId}:${i.bio.positionInChain})`,{atomId:t.id,requested:n,conflictingBondId:e.bond.id})}}for(let r of o){if("numeric"!==r.r1.kind||"numeric"!==r.r2.kind)continue;let o=r.a1.id===e.id&&r.a2.id===t.id&&r.r1.r===i&&r.r2.r===n,s=r.a1.id===t.id&&r.a2.id===e.id&&r.r1.r===n&&r.r2.r===i;if(o||s)throw new P("duplicate-bond",`bond ${e.symbol}:R${i} ↔ ${t.symbol}:R${n} already exists`,{atomId:e.id,bondId:r.id})}}_freeRgroupsOn(e){return cn(e,this._mol.bonds)}addHydrogenBond(e,t){this._ensureLive();let i=new mn(this._mol),n={kind:"pair"},o=i.addBond({a1:e.id,a2:t.id,kind:"hbond",r1:n,r2:n}),{mol:r}=i.commit();this._replaceMol(r,"addHydrogenBond","api");let s=U(r,o);if(void 0===s)throw new Error("HelmEditor.addHydrogenBond: lost bond after commit");return this._events.fire("bond:add",{bond:s,source:"api"}),s}removeBond(e){this._ensureLive();let t="number"==typeof e?e:e.id,i=U(this._mol,t);if(void 0===i)return;let n=new mn(this._mol);n.removeBond(t);let{mol:o}=n.commit();this._replaceMol(o,"removeBond","api"),this._events.fire("bond:remove",{bond:i,source:"api"})}replaceMonomer(e,t){this._ensureLive();let i=W(this._mol,e.id);if(void 0===i)return;let n=i.symbol;if(n===t)return;let o=new mn(this._mol);o.updateAtom(e.id,{symbol:t});let{mol:r}=o.commit(),s=Pe(r,this._service.monomerLib,{mode:"lenient"}).mol;this._replaceMol(s,`replaceMonomer:${n}->${t}`,"api");let a=W(s,e.id);void 0!==a&&this._events.fire("monomer:replace",{atom:a,oldSymbol:n,newSymbol:t})}hitTest(e,t){this._ensureLive();let i=new bn(this._mol,this._theme).test({x:e,y:t});return null===i?null:void 0!==i.atom?{atom:i.atom}:void 0!==i.bond?{bond:i.bond}:null}moveAtom(e,t){this._ensureLive();let i=W(this._mol,e);if(void 0===i||i.p.x===t.x&&i.p.y===t.y)return;let n=new mn(this._mol);n.updateAtom(e,{p:{x:t.x,y:t.y}});let{mol:o}=n.commit();this._replaceMol(o,"moveAtom","user")}moveAtoms(e){if(this._ensureLive(),0===e.length)return;let t=new mn(this._mol),i=0;for(let n of e){let e=W(this._mol,n.atomId);void 0!==e&&(e.p.x===n.p.x&&e.p.y===n.p.y||(t.updateAtom(n.atomId,{p:{x:n.p.x,y:n.p.y}}),i+=1))}if(0===i)return;let{mol:n}=t.commit();this._replaceMol(n,"moveAtom","user")}cleanLayout(e){this._ensureLive(),this._resetLastAction();let t=Ut(this._mol,void 0!==this._options.bondLength?{bondLength:this._options.bondLength}:void 0);this._mol=t,this._history.push({mol:t,label:"cleanLayout"}),this._events.fire("layout:change",{mol:t,strategy:"auto"}),this._events.fire("mol:changed",{mol:t,changedAtomIds:new Set(t.atoms.map(e=>e.id)),changedBondIds:to,reason:"cleanLayout"})}canUndo(){return this._history.canUndo()}canRedo(){return this._history.canRedo()}undo(){this._ensureLive();let e=this._history.undo();null!==e&&this._restoreFromHistory(e.mol,"undo")}redo(){this._ensureLive();let e=this._history.redo();null!==e&&this._restoreFromHistory(e.mol,"redo")}on(e,t){return this._events.on(e,t)}off(e,t){this._events.off(e,t)}fire(e,t){this._events.fire(e,t)}zoom(e,t){if(this._ensureLive(),!Number.isFinite(e)||e<=0)return;let i=this._viewport.scale,n=Math.min(8,Math.max(.2,i*e));if(n===i)return;let o={...this._viewport.offset},r=o;void 0!==t&&(r={x:o.x+(i-n)*t.x,y:o.y+(i-n)*t.y});let s={scale:n,offset:r};this._viewport=s;let a=t??{x:0,y:0};this._events.fire("view:zoom",{scale:n,center:a,previousScale:i}),this._events.fire("view:viewport-change",{viewport:s})}panTo(e){this._ensureLive();let t={...this._viewport.offset},i={scale:this._viewport.scale,offset:{...e}};this._viewport=i,this._events.fire("view:pan",{offset:i.offset,previousOffset:t}),this._events.fire("view:viewport-change",{viewport:i})}getViewport(){return{scale:this._viewport.scale,offset:{...this._viewport.offset}}}fitToContent(e){this._ensureLive();let t=0,i=0,n=0,o=0,r=!1;for(let e of this._mol.atoms)r?(e.p.x<t&&(t=e.p.x),e.p.x>n&&(n=e.p.x),e.p.y<i&&(i=e.p.y),e.p.y>o&&(o=e.p.y)):(t=n=e.p.x,i=o=e.p.y,r=!0);let s=r?{x:t,y:i,width:n-t,height:o-i}:{x:0,y:0,width:0,height:0},a={...this._viewport.offset},l=this._viewport.scale,h={scale:1,offset:{x:0,y:0}};this._viewport=h,1!==l&&this._events.fire("view:zoom",{scale:1,center:{x:0,y:0},previousScale:l}),(0!==a.x||0!==a.y)&&this._events.fire("view:pan",{offset:h.offset,previousOffset:a}),this._events.fire("view:viewport-change",{viewport:h}),this._events.fire("view:fit-to-content",{bbox:s})}setViewOnly(e){this._ensureLive();let t=this._viewOnly;t!==e&&(this._viewOnly=e,this._events.fire("option:change",{key:"viewOnly",oldValue:t,newValue:e}))}setTheme(e){this._ensureLive();let t=this._theme;t!==e&&(this._theme=e,this._events.fire("theme:change",{theme:e,previousTheme:t}))}toSvg(e){this._ensureLive();let t=this.getHelm(),i={};return void 0!==e?.width&&(i.width=e.width),void 0!==e?.height&&(i.height=e.height),this._service.renderToSvg(t,i)}async toPng(e){this._ensureLive();let t=this.getHelm(),i={};return void 0!==e?.width&&(i.width=e.width),void 0!==e?.height&&(i.height=e.height),this._service.renderToPng(t,i)}_getHost(){return this._host}_observerCount(){return this._events.observerCount()}_currentHighlights(){return this._highlights}_currentTheme(){return this._theme}_getView(){return this._view}_getViewport(){return this._viewport}openAtomProps(e){this._ensureLive(),null!==this._host&&(null===this._atomDialog&&(this._atomDialog=new Xn(this)),this._atomDialog.open(e))}openBondProps(e){this._ensureLive(),null!==this._host&&(null===this._bondDialog&&(this._bondDialog=new Qn(this)),this._bondDialog.open(e))}openFindReplace(){this._ensureLive(),null!==this._host&&(null===this._findReplaceDialog&&(this._findReplaceDialog=new eo(this)),this._findReplaceDialog.open())}getMode(){return this._mode}setMode(e){this._ensureLive();let t=this._mode;t!==e&&(this._mode=e,this._events.fire("option:change",{key:"mode",oldValue:t,newValue:e}))}getNextAddSymbol(){return this._nextAdd}setNextAddSymbol(e,t){this._ensureLive();let i=this._nextAdd;if(null===e)this._nextAdd=null;else{if(void 0===t)return;this._nextAdd={symbol:e,biotype:t}}this._events.fire("option:change",{key:"nextAdd",oldValue:i,newValue:this._nextAdd})}startPaletteDrag(e,t){this._ensureLive(),null!==this._dnd?this._dnd.startPaletteDrag(e,t):this._events.fire("dnd:start",{source:"palette",symbol:e})}findMonomers(e){this._ensureLive();let t=[];for(let i of this._mol.atoms)i.symbol===e&&t.push(i);return t}replaceMonomers(e,t){let i,n;if(this._ensureLive(),"string"==typeof e){let o=e,r=t;if(i=this.findMonomers(o),0===i.length)return 0;if(o===r)return i.length;n=`${o}->${r}`}else{let o=t,r=new Set,s=[];for(let t of e){if(r.has(t.id))continue;r.add(t.id);let e=W(this._mol,t.id);void 0!==e&&e.symbol!==o&&s.push(e)}if(0===s.length)return 0;i=s,n=`atoms[${s.length}]->${o}`}let o=t,r=new mn(this._mol);for(let e of i)r.updateAtom(e.id,{symbol:o});let{mol:s}=r.commit(),a=Pe(s,this._service.monomerLib,{mode:"lenient"}).mol;return this._replaceMol(a,`replaceMonomers:${n}`,"api"),i.length}nudgeSelection(e,t){this._ensureLive();let i=this._selection;if(0===i.atoms.size)return;let n=new mn(this._mol);for(let o of i.atoms){let i=W(this._mol,o);void 0!==i&&n.updateAtom(o,{p:{x:i.p.x+e,y:i.p.y+t}})}let{mol:o}=n.commit();this._replaceMol(o,"nudge","user")}deleteSelection(){this._ensureLive();let e=this._selection;if(0===e.atoms.size&&0===e.bonds.size)return;let t=new mn(this._mol);for(let i of e.atoms)t.removeAtom(i);for(let i of e.bonds)t.removeBond(i);let{mol:i}=t.commit();this._selection=hn.empty(),this._replaceMol(i,"delete-selection","user"),this._events.fire("selection:change",{selection:this._selection,addedAtomIds:to,removedAtomIds:e.atoms,addedBondIds:to,removedBondIds:e.bonds})}appendRnaTriplet(e,t,i){this._ensureLive();let n=oo(e,t,i),o=function(e,t){if(""===e)return`RNA1{${t}}$$$$V2.0`;let i,n=/(^|\|)(RNA\d+)\{([^}]*)\}/g,o=null;for(;null!==(i=n.exec(e));)o={name:i[2],body:i[3],matchText:i[0]};if(null!==o){let i=""===o.body?"":".",n=`${o.matchText.startsWith("|")?"|":""}${o.name}{${o.body}${i}${t}}`,r=e.lastIndexOf(o.matchText);return e.slice(0,r)+n+e.slice(r+o.matchText.length)}let r,s=new Set,a=/RNA(\d+)\{/g;for(;null!==(r=a.exec(e));)s.add(Number(r[1]));let l=1;for(;s.has(l);)l+=1;let h=`RNA${l}{${t}}`,d=e.indexOf("$");if(d<0)return`${e}|${h}$$$$V2.0`;let c=e.slice(0,d);return`${c}${""===c?"":"|"}${h}${e.slice(d)}`}(this.getHelm(),n);this.setHelm(o)}placeRnaTriplet(e,t,i){this._ensureLive();let n,o=1.6*(this._options.bondLength??28),r=this._mol.atoms;if("add-triplet"===this._lastAction&&null!==this._lastTripletSugarPos)n={x:this._lastTripletSugarPos.x+2*o,y:this._lastTripletSugarPos.y};else if(0===r.length)n={x:0,y:0};else{let e=r[0].p.x,t=r[0].p.y;for(let i of r)i.p.x<e&&(e=i.p.x),i.p.y>t&&(t=i.p.y);n={x:e,y:t+o}}let s={x:n.x+o,y:n.y},a={x:n.x,y:n.y+o},l=new Set;for(let e of this._mol.chains)l.add(e.id);let h=1;for(;l.has(`RNA${h}`);)h+=1;let d=`RNA${h}`,c=new mn(this._mol),u=c.addAtom({p:n,biotype:Q,symbol:e,chainId:d,positionInChain:1}),p=c.addAtom({p:s,biotype:J,symbol:i,chainId:d,positionInChain:2}),m=c.addAtom({p:a,biotype:Z,symbol:t,chainId:d,positionInChain:0});c.addBond({a1:u,a2:m,kind:"branch",r1:{kind:"numeric",r:3},r2:{kind:"numeric",r:1}}),c.addBond({a1:u,a2:p,kind:"backbone",r1:{kind:"numeric",r:2},r2:{kind:"numeric",r:1}});let{mol:f}=c.commit(),b=Pe(this._postProcessTripletMol(f,u,m,d),this._service.monomerLib,{mode:"lenient"}).mol;this._replaceMol(b,"placeRnaTriplet","user"),this._lastAction="add-triplet",this._lastTripletSugarPos=n}_postProcessTripletMol(e,t,i,n){let o=new Map,r=W(e,i),s=W(e,t);if(void 0===r||void 0===s)return e;let a={...s,branchAtom:r};o.set(t,a);let l=e.bonds.map(e=>{let t=o.get(e.a1.id)??e.a1,i=o.get(e.a2.id)??e.a2;return t===e.a1&&i===e.a2?e:{...e,a1:t,a2:i}}),h=new Map;for(let e of l)h.set(e.id,e);let d=e.chains.map(e=>{let t=[];for(let r of e.backboneAtoms)e.id===n&&r.id===i||t.push(o.get(r.id)??r);let r=e.bonds.map(e=>h.get(e.id)??e);return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:r,...void 0!==e.annotation?{annotation:e.annotation}:{}}}),c={atoms:e.atoms.map(e=>o.get(e.id)??e),bonds:l,chains:d,groups:e.groups,annotations:e.annotations};return c=this._refreshContinuousIdsLocal(c),c}_resetLastAction(){this._lastAction="other",this._lastTripletSugarPos=null}_ensureLive(){if(this._destroyed)throw new Error("HelmEditor: this instance has been destroyed.")}_replaceMol(e,t,i){let n=this._service.serialize(this._mol),o=this._service.serialize(e);this._mol=e,this._history.push({mol:e,label:t}),this._resetLastAction(),this._events.fire("mol:changed",{mol:e,changedAtomIds:new Set(e.atoms.map(e=>e.id)),changedBondIds:new Set(e.bonds.map(e=>e.id)),reason:t}),n!==o&&this._events.fire("helm:changed",{helm:o,mol:e,source:i})}_restoreFromHistory(e,t){let i=this._service.serialize(this._mol),n=this._service.serialize(e);this._mol=e,this._resetLastAction(),this._events.fire("mol:changed",{mol:e,changedAtomIds:new Set(e.atoms.map(e=>e.id)),changedBondIds:new Set(e.bonds.map(e=>e.id)),reason:t}),i!==n&&this._events.fire("helm:changed",{helm:n,mol:e,source:t})}};function no(e){return e.startsWith("[")&&e.endsWith("]")||1===e.length&&/^[A-Za-z]$/.test(e)?e:`[${e}]`}function oo(e,t,i){return`${no(e)}(${no(t)})${no(i)}`}var ro="http://www.w3.org/2000/svg",so={sugar:Q,base:Z,linker:J},ao={sugar:["r","R"],base:["A"],linker:["p","P"]},lo={x:70,y:60},ho={x:140,y:60},co={x:70,y:130},uo=class e{constructor(e,t,i){this.onValueSet=new ae,this.onPickModeChange=new ae,this._slots=new Map,this._favStar=null,this._pickMode=null,this._destroyed=!1,this._builderRdkitCache=new Map,this._editor=t,this._doc=i?.documentImpl??vn(e),this._hooks=i?.paletteHooks??null,this._favHooks=i?.favoriteHooks??null,this.element=wn(this._doc,"div",{class:"hw-rna-builder","data-testid":"rna-builder"});let n=wn(this._doc,"div",{class:"hw-rna-builder__header"});if(n.appendChild(wn(this._doc,"div",{class:"hw-rna-builder__title"},["RNA builder"])),null!==this._favHooks){let e=wn(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"},["☆"]),t=e=>{e.stopPropagation();let t=this.getSelection();""===t.preview||null===this._favHooks||this._favHooks.toggleFavoriteTriplet(t.sugar,t.base,t.linker)};e.addEventListener("click",t),e.addEventListener("keydown",e=>{let i=e;("Enter"===i.key||" "===i.key)&&t(e)}),this._favStar=e,n.appendChild(e)}this.element.appendChild(n),this._hintEl=wn(this._doc,"div",{class:"hw-rna-builder__hint","data-testid":"rna-builder-hint",hidden:!0}),this.element.appendChild(this._hintEl);let o=this._buildSvg();this.element.appendChild(o),this._preview=wn(this._doc,"div",{class:"hw-rna-builder__preview","data-testid":"rna-builder-preview"}),this.element.appendChild(this._preview),this._addBtn=wn(this._doc,"button",{class:"hw-rna-builder__add",type:"button","data-testid":"rna-builder-add-btn"},["Add triplet"]),this._addBtn.addEventListener("click",()=>this._onAddClicked()),this.element.appendChild(this._addBtn),e.appendChild(this.element);let r=t.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),s=t.on("theme:change",()=>{this._destroyed||this._repaintSlotColors()});this._libUnsub=()=>{try{r()}catch{}try{s()}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}getSelection(){let e=this._slots.get("sugar")?.value??"",t=this._slots.get("base")?.value??"",i=this._slots.get("linker")?.value??"";return{sugar:e,base:t,linker:i,preview:""!==e&&""!==t&&""!==i?oo(e,t,i):""}}setField(e,t){let i=this._slots.get(e);void 0!==i&&(i.value=t,this._setLabelText(i.labelEl,t),this._repaintSlot(i),this._updatePreview(),this.onValueSet.next({field:e,symbol:t}))}startPickMode(e){this._pickMode!==e?(null!==this._pickMode&&this._setSlotPressed(this._pickMode,!1),this._pickMode=e,this._setSlotPressed(e,!0),this._setHintActive(e),this.onPickModeChange.next({field:e}),null!==this._hooks&&this._hooks.beginBiotypeFilter(so[e],t=>{this.setField(e,t),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 e=this._doc.createElementNS(ro,"svg");e.setAttribute("class","hw-rna-builder__triplet"),e.setAttribute("viewBox","0 0 200 180"),e.setAttribute("data-testid","rna-builder-triplet-svg"),e.setAttribute("role","group"),e.setAttribute("aria-label","Triplet preview");let t=this._doc.createElementNS(ro,"line");t.setAttribute("class","hw-rna-builder__bond"),t.setAttribute("x1",String(lo.x+18)),t.setAttribute("y1",String(lo.y)),t.setAttribute("x2",String(ho.x-18)),t.setAttribute("y2",String(ho.y)),e.appendChild(t);let i=this._doc.createElementNS(ro,"line");i.setAttribute("class","hw-rna-builder__bond"),i.setAttribute("x1",String(lo.x)),i.setAttribute("y1",String(lo.y+18)),i.setAttribute("x2",String(co.x)),i.setAttribute("y2",String(co.y-22)),e.appendChild(i);let n=this._doc.createElementNS(ro,"rect");n.setAttribute("class","hw-rna-builder__slot-shape"),n.setAttribute("x",String(-18)),n.setAttribute("y",String(-18)),n.setAttribute("width",String(36)),n.setAttribute("height",String(36)),n.setAttribute("rx","8"),n.setAttribute("ry","8");let o=this._buildSlot("sugar","Pick sugar (backbone)",lo,n),r=this._doc.createElementNS(ro,"circle");r.setAttribute("class","hw-rna-builder__slot-shape"),r.setAttribute("cx","0"),r.setAttribute("cy","0"),r.setAttribute("r",String(18));let s=this._buildSlot("linker","Pick linker",ho,r),a=this._doc.createElementNS(ro,"path");a.setAttribute("class","hw-rna-builder__slot-shape"),a.setAttribute("d","M -22 0 L 0 -22 L 22 0 L 0 22 Z");let l=this._buildSlot("base","Pick base",co,a);return e.appendChild(s.groupEl),e.appendChild(o.groupEl),e.appendChild(l.groupEl),this._slots.set("sugar",o),this._slots.set("linker",s),this._slots.set("base",l),e}_buildSlot(e,t,i,n){let o=this._doc.createElementNS(ro,"g");o.setAttribute("class","hw-rna-builder__slot"),o.setAttribute("data-slot",e),o.setAttribute("data-testid",`rna-builder-slot-${e}`),o.setAttribute("role","button"),o.setAttribute("tabindex","0"),o.setAttribute("aria-label",t),o.setAttribute("aria-pressed","false"),o.setAttribute("transform",`translate(${i.x} ${i.y})`),o.appendChild(n);let r=this._doc.createElementNS(ro,"text");r.setAttribute("class","hw-rna-builder__slot-label"),r.setAttribute("data-testid",`rna-builder-${e}-value`),r.setAttribute("x","0"),r.setAttribute("y","0"),r.setAttribute("text-anchor","middle"),r.setAttribute("dominant-baseline","central"),o.appendChild(r);let s=t=>{t.stopPropagation(),this.startPickMode(e)};return o.addEventListener("click",s),o.addEventListener("keydown",e=>{let t=e;("Enter"===t.key||" "===t.key)&&s(e)}),o.addEventListener("mouseenter",t=>this._showSlotTooltip(e,t)),o.addEventListener("mouseleave",()=>this._hideSlotTooltip()),o.addEventListener("focus",()=>this._showSlotTooltip(e,null)),o.addEventListener("blur",()=>this._hideSlotTooltip()),{id:e,biotype:so[e],groupEl:o,shapeEl:n,labelEl:r,value:""}}_setLabelText(e,t){let i=[];for(let t=e.firstChild;null!==t;t=t.nextSibling)"title"===t.nodeName||"TITLE"===t.nodeName||i.push(t);for(let t of i)e.removeChild(t);let n=function(e){let t=e.length;return t<=2?16:t<=4?11:t<=7?8:t<=10?6:5}(t);e.setAttribute("font-size",String(n)),e.setAttribute("text-anchor","middle"),e.setAttribute("dominant-baseline","central");let o=t.length>10?`${t.slice(0,9)}…`:t;e.appendChild(this._doc.createTextNode(o));let r=e.parentNode;if(null!==r){let e=null;for(let t=r.firstChild;null!==t;t=t.nextSibling)if("title"===t.nodeName||"TITLE"===t.nodeName){e=t;break}for(null===e&&(e=this._doc.createElementNS(ro,"title"),r.insertBefore(e,r.firstChild));null!==e.firstChild;)e.removeChild(e.firstChild);e.appendChild(this._doc.createTextNode(t))}}_repaintSlotColors(){for(let e of this._slots.values())this._repaintSlot(e)}_repaintSlot(e){let t=this._editor.getService().monomerLib,i=this._theme(),n=""===e.value?null:function(e,t,i){return e.getMonomerSet(t).get(i)??null}(t,e.biotype,e.value),o=Ie(n,e.biotype,i.colorTheme);e.shapeEl.style.fill=o.background,e.shapeEl.style.stroke=o.line,e.labelEl.style.fill=o.text}_populateDefaults(){let e=this._editor.getService().monomerLib;for(let[t,i]of this._slots.entries()){let n=mo(e,i.biotype),o=fo(n,ao[t]),r=""!==i.value&&n.some(e=>e.symbol===i.value)?i.value:o??n[0]?.symbol??"";i.value=r,this._setLabelText(i.labelEl,r)}}_updatePreview(){let e=this.getSelection();for(;null!==this._preview.firstChild;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(""===e.preview?"-":e.preview)),this._updateFavStar(e)}_updateFavStar(e){if(null===this._favStar||null===this._favHooks)return;let t=""!==e.preview,i=t&&this._favHooks.isFavoriteTriplet(e.sugar,e.base,e.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"),t?this._favStar.removeAttribute("aria-disabled"):this._favStar.setAttribute("aria-disabled","true");let n="hw-rna-builder__fav"+(i?" hw-rna-builder__fav--active":"")+(t?"":" hw-rna-builder__fav--disabled");this._favStar.setAttribute("class",n)}_onAddClicked(){let e=this.getSelection();""!==e.preview&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)}_exitPickMode(){if(null===this._pickMode)return;let e=this._pickMode;this._setSlotPressed(e,!1),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null})}_setHintActive(e){let t=this._hintEl;for(;null!==t.firstChild;)t.removeChild(t.firstChild);if(null===e)return void t.setAttribute("hidden","");t.removeAttribute("hidden");let i="sugar"===e?"sugar":"base"===e?"base":"linker";t.appendChild(this._doc.createTextNode(`Pick ${i} from palette`))}_setSlotPressed(e,t){let i=this._slots.get(e);if(void 0===i)return;i.groupEl.setAttribute("aria-pressed",t?"true":"false");let n=(i.groupEl.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-rna-builder__slot--active"!==e).join(" ");i.groupEl.setAttribute("class",t?`${n} hw-rna-builder__slot--active`:n)}_theme(){let e=this._editor;return"function"==typeof e._currentTheme?e._currentTheme():this._editor.getService().theme}_rdkit(){let e=this._editor.getService().options?.rdkitModule;return e??null}_builderRdkitSvgFor(t){if(null===t)return null;let i=t.smiles;if(void 0===i||""===i)return null;let n=this._rdkit();if(null===n)return null;let o=`${t.polymerType}:${t.symbol}`;if(this._builderRdkitCache.has(o))return this._builderRdkitCache.get(o)??null;let r=xn(n,i,220,140);if(this._builderRdkitCache.size>=e._BUILDER_RDKIT_CACHE_LIMIT){let e=this._builderRdkitCache.keys().next().value;void 0!==e&&this._builderRdkitCache.delete(e)}return this._builderRdkitCache.set(o,r),r}_slotHint(e){switch(e){case"sugar":return"Click to choose a different sugar";case"base":return"Click to choose a different base";case"linker":return"Click to choose a different linker"}}_slotTitle(e,t){let i=""===t?"?":t;switch(e){case"sugar":return`Sugar: ${i}`;case"base":return`Base: ${i}`;case"linker":return`Linker: ${i}`}}_showSlotTooltip(e,t){let i=this._slots.get(e);if(void 0===i)return;let n=this._editor.getService().monomerLib.getMonomerSet(i.biotype),o=""===i.value?null:n.get(i.value)??null,r=Cn(this._doc,"builder-tooltip","hw-builder-tooltip");En(this._doc,r,{symbol:this._slotTitle(e,i.value),name:o?.name??"",rdkitSvg:this._builderRdkitSvgFor(o),rdkitTestid:"builder-tooltip-rdkit-svg",hint:this._slotHint(e)});let s=t;if(null!==s&&"number"==typeof s.clientX&&"number"==typeof s.clientY)kn(r,s.clientX,s.clientY);else{let e=i.groupEl,t="function"==typeof e.getBoundingClientRect?e.getBoundingClientRect():null;null!==t?kn(r,t.left+t.width/2,t.top+t.height/2):kn(r,0,0)}}_hideSlotTooltip(){Bn(this._doc.body.querySelector('[data-testid="builder-tooltip"]'))}};uo._BUILDER_RDKIT_CACHE_LIMIT=256;var po=uo;function mo(e,t){let i=e.getMonomerSet(t),n=[];for(let e of i.values())n.push(e);return n.sort((e,t)=>e.symbol.localeCompare(t.symbol)),n}function fo(e,t){let i=new Set;for(let t of e)i.add(t.symbol);for(let e of t)if(i.has(e))return e;return null}var bo="Favorites",go={[bo]:"★ Favorites",[ne.PEPTIDE]:"Peptides",[ne.RNA]:"RNA",[ne.CHEM]:"CHEM",[ne.BLOB]:"BLOB",G:"G"},Ao=[bo,ne.PEPTIDE,ne.RNA,ne.CHEM,ne.BLOB,"G"],_o="hwe:palette:favorites",yo="hwe:palette:active-tab";function vo(e){return`${e.sugar}|${e.base}|${e.linker}`}var wo=class e{constructor(e,t,i){this.favoritesChanged=new ae,this._nextAddUnsub=()=>{},this._favorites=new Set,this._favoriteTriplets=[],this._pendingRnaSelection=null,this._visibleTabs=[bo],this._activeTab=bo,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=t,this._doc=i?.documentImpl??vn(e),this._opts={documentImpl:this._doc,groupByNaturalAnalog:i?.groupByNaturalAnalog??!0,allowFavorites:i?.allowFavorites??!0},this._loadFavorites(),this._activeTab=this._resolveInitialTab(i?.initialTab),this.element=wn(this._doc,"div",{class:"hw-palette","data-testid":"palette"}),e.appendChild(this.element),this._render(),this._libUnsub=t.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),this._themeUnsub=t.on("theme:change",()=>{this._destroyed||this.refresh()}),this._nextAddUnsub=t.on("option:change",e=>{this._destroyed||"nextAdd"===e.key&&this._updatePrimedClasses()})}refresh(){this._render()}setFilter(e){this._filter=e.trim().toLowerCase(),null!==this._searchInput&&this._searchInput.value!==e&&(this._searchInput.value=e),this._applyFilter()}setActiveTab(e){this._visibleTabs.includes(e)&&(this._activeTab=e,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter())}getActiveTab(){return this._activeTab}getFavorites(){let e=this._editor.getService().monomerLib,t=[];for(let i of this._favorites)null!==this._findMonomer(e,i)&&t.push(i);return t}setFavorite(e,t){t!==this._favorites.has(e)&&(t?this._favorites.add(e):this._favorites.delete(e),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(e=>({...e}))}isFavoriteTriplet(e,t,i){let n=vo({sugar:e,base:t,linker:i});return this._favoriteTriplets.some(e=>vo(e)===n)}setFavoriteTriplet(e,t,i,n){let o=vo({sugar:e,base:t,linker:i}),r=this._favoriteTriplets.findIndex(e=>vo(e)===o);n!==r>=0&&(n?this._favoriteTriplets.push({sugar:e,base:t,linker:i}):this._favoriteTriplets.splice(r,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}_hidePaletteTooltips(){let e=this._doc.body;Bn(e.querySelector('[data-testid="palette-tooltip"]')),Bn(e.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 e=this._pickCanceller;this._teardownPickMode(),e?.()}_buildPaletteFilterHooks(){return{beginBiotypeFilter:(e,t,i)=>{null!==this._activeBiotypeFilter&&this._teardownPickMode(),this._activeBiotypeFilter=e,this._pickResolver=t,this._pickCanceller=i,this._applyFilter();let n=e=>{"Escape"===e.key&&this.cancelBiotypeFilter()};this._pickEscapeListener=n,this._doc.defaultView?.addEventListener("keydown",n);let o=e=>{if(null===this._activeBiotypeFilter)return;let t=e.target;if(null==t)return;let i=this._activeBiotypeFilter,n=t;for(;null!==n;){let e=void 0===n.getAttribute?null:n.getAttribute("class");if(null!==e){let t=e.split(/\s+/);if(t.includes("hw-palette__tile")){if((n.getAttribute("data-biotype")??"")===i)return;break}if(t.includes("hw-rna-builder__slot")){if(this._isInsideOwnPalette(n))return;break}}n=n.parentElement}this.cancelBiotypeFilter()};this._pickOutsideClickListener=o,this._doc.addEventListener("mousedown",o,!0)},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let e=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`);if(null===e)return;let t=e;try{if("function"==typeof t.scrollTo)return void t.scrollTo({top:0,behavior:"smooth"})}catch{}"number"==typeof t.scrollTop&&(t.scrollTop=0)}_isInsideOwnPalette(e){let t=e;for(;null!==t;){if(t===this.element)return!0;t=t.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 e=this._doc.createElement("input");e.setAttribute("type","search"),e.setAttribute("class","hw-palette__search"),e.setAttribute("placeholder","Search monomers..."),e.setAttribute("data-testid","palette-search"),""!==this._filter&&(e.value=this._filter),e.addEventListener("input",()=>this.setFilter(e.value)),this._searchInput=e,this.element.appendChild(e),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=bo);let t=wn(this._doc,"div",{class:"hw-palette__tabs",role:"tablist","data-testid":"palette-tabs"});for(let e of this._visibleTabs){let i=e===this._activeTab,n=wn(this._doc,"button",{class:"hw-palette__tab",type:"button",role:"tab","aria-controls":`hw-palette-pane-${e}`,"aria-selected":i?"true":"false","data-testid":`palette-tab-${e}`,"data-tab":e,title:go[e]},[go[e]]);n.addEventListener("click",()=>this.setActiveTab(e)),t.appendChild(n)}this.element.appendChild(t);let i=wn(this._doc,"div",{class:"hw-palette__panes"}),n=this._theme(),o=this._editor.getService().monomerLib;for(let e of this._visibleTabs){let t=e===this._activeTab,r=wn(this._doc,"div",{class:"hw-palette__pane",id:`hw-palette-pane-${e}`,role:"tabpanel","data-testid":`palette-pane-${e}`,"data-tab":e,hidden:!t});e===bo?this._buildFavoritesPane(r,o,n):this._buildPolymerPane(r,e,o,n),i.appendChild(r)}this.element.appendChild(i),this._applyFilter()}_computeVisibleTabs(){let e=this._editor.getService().monomerLib,t=new Set;for(let i of e.getPolymerTypes())t.add(i);let i=[];i.push(bo);for(let e of Ao)e!==bo&&t.has(e)&&i.push(e);return i}_buildFavoritesPane(e,t,i){let n=this._resolveFavoriteMonomers(t),o=this._favoriteTriplets;if(0===n.length&&0===o.length){let t=wn(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 e.appendChild(t)}for(let[t,i]of this._groupByPolymerAndType(n))e.appendChild(this._renderGroup(t,i));o.length>0&&e.appendChild(this._renderTripletGroup("RNA · Triplets",o,t))}_groupByPolymerAndType(e){let t=new Map;for(let i of e){let e=i.polymerType,n=i.monomerType??"Undefined",o=`${e}|${n}`,r=t.get(o);void 0===r&&(r={pt:e,mt:n,list:[]},t.set(o,r)),r.list.push(i)}let i=e=>{let t=Ao.indexOf(e);return t<0?99:t},n={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(t.values()).sort((e,t)=>i(e.pt)-i(t.pt)||(n[e.mt]??9)-(n[t.mt]??9)||e.mt.localeCompare(t.mt)).map(e=>[`${this._polymerLabel(e.pt)} · ${e.mt}`,e.list])}_polymerLabel(e){return go[e]??e}_renderTripletGroup(e,t,i){let n=wn(this._doc,"div",{class:"hw-palette__group","data-natural-analog":e}),o=wn(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${e}`},[e]),r=wn(this._doc,"div",{class:"hw-triplet-chips","data-testid":"palette-triplet-favorites"});for(let e of t)r.appendChild(this._renderTripletChip(e,i));return n.appendChild(o),n.appendChild(r),n}_renderTripletChip(e,t){let i=oo(e.sugar,e.base,e.linker),n=t.getMonomerSet(Z).get(e.base)??null,o=Ie(n,Z,this._theme().colorTheme),r=this.isFavoriteTriplet(e.sugar,e.base,e.linker),s=void 0!==n?.name&&""!==n.name?`${i} — ${n.name}`:i,{root:a}=function(e,t){let i=!1!==t.showStar,n=wn(e,"span",{class:"hw-triplet-chip__star"},[t.favorite?"★":"☆"]),o=wn(e,"span",{class:"hw-triplet-chip__label"},[t.label]),r=["hw-triplet-chip"];t.favorite&&r.push("hw-triplet-chip--favorite");let s=i?[n,o]:[o];return{root:wn(e,"div",{class:r.join(" "),role:"button",tabindex:"0","aria-label":t.title,"data-sugar":t.sugar,"data-base":t.base,"data-linker":t.linker,"data-triplet":t.label,"data-testid":`palette-triplet-${t.label}`,title:t.title,style:`background:${t.background};color:${t.textColor};`},s),star:n}}(this._doc,{sugar:e.sugar,base:e.base,linker:e.linker,label:i,title:s,background:be(o.background),textColor:o.text,favorite:r,showStar:this._opts.allowFavorites});return this._wireTripletChip(a,e),a}_wireTripletChip(e,t){e.addEventListener("mouseenter",e=>{let i=e,n=Cn(this._doc,"palette-triplet-tooltip","hw-palette-tooltip hw-triplet-tooltip");(function(e,t,i){for(;null!==t.firstChild;)t.removeChild(t.firstChild);t.appendChild(wn(e,"div",{class:"hw-tooltip__symbol"},[i.title]));let n=wn(e,"div",{class:"hw-tooltip__triplet"});for(let t of i.parts){let o=wn(e,"div",{class:"hw-tooltip__triplet-part"});if(o.appendChild(wn(e,"div",{class:"hw-tooltip__triplet-role"},[`${t.role}: ${t.symbol}`])),void 0!==t.name&&""!==t.name&&t.name!==t.symbol&&o.appendChild(wn(e,"div",{class:"hw-tooltip__name"},[t.name])),void 0!==t.rdkitSvg&&null!==t.rdkitSvg&&""!==t.rdkitSvg){let n={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(n["data-testid"]=i.rdkitTestid);let r=wn(e,"div",n);r.innerHTML=t.rdkitSvg,o.appendChild(r)}n.appendChild(o)}t.appendChild(n),void 0!==i.hint&&""!==i.hint&&t.appendChild(wn(e,"div",{class:"hw-tooltip__hint"},[i.hint]))})(this._doc,n,{title:oo(t.sugar,t.base,t.linker),parts:this._tripletTooltipParts(t),hint:"Click to add this triplet",rdkitTestid:"palette-triplet-tooltip-rdkit-svg"}),kn(n,"number"==typeof i.clientX?i.clientX:0,"number"==typeof i.clientY?i.clientY:0)}),e.addEventListener("mouseleave",()=>{Bn(this._doc.body.querySelector('[data-testid="palette-triplet-tooltip"]'))}),e.addEventListener("click",e=>{let i=e.target;if(this._opts.allowFavorites&&!0===i?.classList?.contains("hw-triplet-chip__star"))return this.setFavoriteTriplet(t.sugar,t.base,t.linker,!this.isFavoriteTriplet(t.sugar,t.base,t.linker)),void e.stopPropagation();this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)}),e.addEventListener("keydown",e=>{let i=e;("Enter"===i.key||" "===i.key)&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)})}_buildRnaDefaultChips(t){let i=this._pickSymbol(t.getMonomerSet(Q),["r","R"]),n=this._pickSymbol(t.getMonomerSet(J),["p","P"]),o=t.getMonomerSet(Z);if(null===i||null===n)return null;let r=e._DEFAULT_TRIPLET_BASES.filter(e=>o.has(e));if(0===r.length)return null;let s=wn(this._doc,"div",{class:"hw-triplet-chips hw-triplet-chips--defaults","data-testid":"rna-default-triplets"});for(let e of r)s.appendChild(this._renderTripletChip({sugar:i,base:e,linker:n},t));return s}_tripletTooltipParts(e){let t=this._editor.getService().monomerLib,i=(e,i,n)=>{let o=t.getMonomerSet(i).get(n)??null;return{role:e,symbol:n,...void 0!==o?.name?{name:o.name}:{},rdkitSvg:null===o?null:this._paletteRdkitSvg(o)}};return[i("Sugar",Q,e.sugar),i("Base",Z,e.base),i("Linker",J,e.linker)]}_pickSymbol(e,t){for(let i of t)if(e.has(i))return i;let i=e.keys().next();return!0===i.done?null:i.value}_restoreRnaSelection(){let e=this._pendingRnaSelection;if(this._pendingRnaSelection=null,null===e||null===this._rnaBuilder)return;let t=this._editor.getService().monomerLib;""!==e.sugar&&t.getMonomerSet(Q).has(e.sugar)&&this._rnaBuilder.setField("sugar",e.sugar),""!==e.base&&t.getMonomerSet(Z).has(e.base)&&this._rnaBuilder.setField("base",e.base),""!==e.linker&&t.getMonomerSet(J).has(e.linker)&&this._rnaBuilder.setField("linker",e.linker)}_resolveFavoriteMonomers(e){let t=[];for(let i of this._favorites){let n=this._findMonomer(e,i);null!==n&&t.push(n)}return t}_findMonomer(e,t){for(let i of e.getPolymerTypes()){let n=e.getMonomer(i,t);if(null!==n)return n}return null}_buildPolymerPane(e,t,i,n){let o=t,r=this._monomersForPolymer(o,i);if(0===r.length)return;if(o===ne.RNA){this._rnaBuilder=new po(e,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(e,t,i)=>this.isFavoriteTriplet(e,t,i),toggleFavoriteTriplet:(e,t,i)=>this.setFavoriteTriplet(e,t,i,!this.isFavoriteTriplet(e,t,i))}:null}),this._restoreRnaSelection();let t=this._buildRnaDefaultChips(i);null!==t&&e.appendChild(t);let n=this._groupRna(r);for(let[t,i]of n)0!==i.length&&e.appendChild(this._renderGroup(t,i));return}if(o===ne.PEPTIDE&&this._opts.groupByNaturalAnalog){let t=this._groupByAnalog(r);for(let[i,n]of t){let t=""===i?"Other":i;e.appendChild(this._renderGroup(t,n))}return}let s=wn(this._doc,"div",{class:"hw-palette__group-tiles"}),a=this._editor.getNextAddSymbol(),l=this._sortByColor(r);for(let e of l){let t=this._biotype(e,o);s.appendChild(this._renderTile(e,t,a))}e.appendChild(s)}_renderGroup(e,t){let i=wn(this._doc,"div",{class:"hw-palette__group","data-natural-analog":e}),n=wn(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${e}`},[e]),o=wn(this._doc,"div",{class:"hw-palette__group-tiles"}),r=this._editor.getNextAddSymbol(),s=this._sortByColor(t);for(let e of s){let t=this._biotype(e,e.polymerType);o.appendChild(this._renderTile(e,t,r))}return i.appendChild(n),i.appendChild(o),i}_sortByColor(e){let t=this._theme(),i=e.map((e,i)=>{let n=function(e){let t=de(e);if(null===t)return{h:0,s:0,l:0};let[i,n,o]=pe(t[0],t[1],t[2]);return{h:i,s:n,l:o}}(Ie(e,this._biotype(e,e.polymerType),t.colorTheme).background),o=0===n.s?1:0;return{m:e,idx:i,h:n.h,s:n.s,l:n.l,isGrey:o}});return i.sort((e,t)=>e.isGrey!==t.isGrey?e.isGrey-t.isGrey:e.h!==t.h?e.h-t.h:e.s!==t.s?e.s-t.s:e.l!==t.l?e.l-t.l:e.idx-t.idx),i.map(e=>e.m)}_monomersForPolymer(e,t){let i=t.getMonomerSymbolsByType(e),n=[];for(let o of i){let i=t.getMonomer(e,o);null!==i&&n.push(i)}return n.sort((e,t)=>e.symbol.localeCompare(t.symbol)),n}_groupByAnalog(e){let t=new Map;for(let i of e){let e=i.naturalAnalog??"",n=t.get(e);void 0===n&&(n=[],t.set(e,n)),n.push(i)}let i=[],n=Array.from(t.keys()).sort((e,t)=>""===e&&""!==t?1:""===t&&""!==e?-1:e.localeCompare(t));for(let e of n)i.push([e,t.get(e)]);return new Map(i)}_groupRna(e){let t=[],i=[],n=[],o=[];for(let r of e){let e=$e(r);e===Q?t.push(r):e===Z?i.push(r):e===J?n.push(r):o.push(r)}let r=new Map;return r.set("Backbones",t),r.set("Bases",i),r.set("Linkers",n),o.length>0&&r.set("Other",o),r}_renderTile(e,t,i){let n=this._favorites.has(e.symbol),o=null!==i&&i.symbol===e.symbol&&i.biotype===t,{root:r,star:s}=function(e,t){let i=Ie(t.monomer,t.biotype,t.theme.colorTheme),n=be(i.background),o=i.text,r=function(e,t){let i=ge(e),n=ge(t);return(Math.max(i,n)+.05)/(Math.min(i,n)+.05)}(o,n)<5,s=t.monomer.symbol,a=function(e){return e<=3?14:e<=6?11:e<=9?9:8}(s.length),l=`font-size:${a}px;${s.length>=10?"line-height:1.1;letter-spacing:-0.02em;":""}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:80px;display:inline-block;`,h=wn(e,"span",{class:"hw-palette__star"},[t.favorite?"★":"☆"]),d=wn(e,"span",{class:"hw-palette__label",style:l},[s]),c=["hw-palette__tile"];t.primed&&c.push("hw-palette__tile--primed"),t.favorite&&c.push("hw-palette__tile--favorite"),r&&c.push("hw-palette__tile--low-contrast");let u=void 0!==t.monomer.name?`${s} — ${t.monomer.name}`:s,p=`background:${n};color:${o};width:100%;min-width:48px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return{root:wn(e,"div",{class:c.join(" "),draggable:"true",role:"button","aria-pressed":t.primed?"true":"false","aria-label":u,"data-symbol":s,"data-biotype":t.biotype,"data-bg":n,"data-raw-bg":i.background,"data-testid":`palette-tile-${s}`,title:u,style:p},[h,d]),star:h}}(this._doc,{monomer:e,biotype:t,theme:this._theme(),favorite:n,primed:o});return this._wireTile(r,s,e,t),r}_rdkit(){let e=this._editor.getService().options?.rdkitModule;return e??null}_paletteRdkitSvg(t){let i=t.smiles;if(void 0===i||""===i)return null;let n=this._rdkit();if(null===n)return null;let o=`${t.polymerType}:${t.symbol}`;if(this._paletteRdkitCache.has(o))return this._paletteRdkitCache.get(o)??null;let r=xn(n,i,220,140);if(this._paletteRdkitCache.size>=e._PALETTE_RDKIT_CACHE_LIMIT){let e=this._paletteRdkitCache.keys().next().value;void 0!==e&&this._paletteRdkitCache.delete(e)}return this._paletteRdkitCache.set(o,r),r}_wireTile(e,t,i,n){e.addEventListener("mouseenter",e=>{let t=e,n=Cn(this._doc,"palette-tooltip","hw-palette-tooltip");En(this._doc,n,{symbol:i.symbol,name:i.name??"",rdkitSvg:this._paletteRdkitSvg(i),rdkitTestid:"palette-tooltip-rdkit-svg"}),kn(n,"number"==typeof t.clientX?t.clientX:0,"number"==typeof t.clientY?t.clientY:0)}),e.addEventListener("mouseleave",()=>{Bn(this._doc.body.querySelector('[data-testid="palette-tooltip"]'))}),e.addEventListener("click",e=>{let t=e.target;if(this._opts.allowFavorites&&void 0!==t&&!0===t?.classList?.contains("hw-palette__star"))return this.setFavorite(i.symbol,!this._favorites.has(i.symbol)),void e.stopPropagation();if(null!==this._activeBiotypeFilter&&this._activeBiotypeFilter===n){let t=this._pickResolver;return this._teardownPickMode(),t?.(i.symbol),this._scrollActivePaneToTop(),void e.stopPropagation()}let o=this._editor.getSelection();if(o.atoms.size>0){let t=this._editor.getMol(),r=[];for(let e of o.atoms){let i=t.atoms.find(t=>t.id===e);void 0!==i&&r.push(i)}return r.length>0&&r.every(e=>e.biotype===n)?(this._editor.replaceMonomers(r,i.symbol),void e.stopPropagation()):(this._editor.fire("editor:status",{message:`Cannot bulk-replace ${r.length} selected atom(s) with ${i.symbol}: selection contains incompatible biotypes for ${n}.`,severity:"warn",durationMs:3e3}),void e.stopPropagation())}let r=this._editor.getNextAddSymbol();if(null!==r&&r.symbol===i.symbol&&r.biotype===n)return this._editor.setNextAddSymbol(null),void this._updatePrimedClasses();this._editor.setNextAddSymbol(i.symbol,n),this._updatePrimedClasses()}),e.addEventListener("dragstart",e=>{let t=e.dataTransfer;if(null!=t)try{t.setData("application/x-hwe-monomer",JSON.stringify({symbol:i.symbol,biotype:n})),t.effectAllowed="copy"}catch{}Bn(this._doc.body.querySelector('[data-testid="palette-tooltip"]')),this._editor.startPaletteDrag(i.symbol,n)})}_biotype(e,t){let i=$e(e);if(null!==i)return i;switch(t){case ne.PEPTIDE:return X;case ne.RNA:return Q;case ne.CHEM:return ee;case ne.BLOB:return te;default:return ee}}_theme(){let e=this._editor;return"function"==typeof e._currentTheme?e._currentTheme():this._editor.getService().theme}_applyFilter(){let e=this._filter,t=this._activeBiotypeFilter,i=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`),n=(i??this.element).querySelectorAll(".hw-palette__tile");for(let i=0;i<n.length;i++){let o=n[i],r=(o.getAttribute("data-symbol")??"").toLowerCase(),s=(o.getAttribute("title")??"").toLowerCase(),a=o.getAttribute("data-biotype")??"",l=(""===e||r.indexOf(e)>=0||s.indexOf(e)>=0)&&(null===t||a===t);o.style.display=l?"":"none"}let o=(i??this.element).querySelectorAll(".hw-triplet-chip");for(let i=0;i<o.length;i++){let n=o[i],r=[n.getAttribute("data-triplet")??"",n.getAttribute("data-sugar")??"",n.getAttribute("data-base")??"",n.getAttribute("data-linker")??""].join(" ").toLowerCase(),s=(""===e||r.indexOf(e)>=0)&&null===t;n.style.display=s?"":"none"}let r=(i??this.element).querySelectorAll(".hw-palette__group");for(let e=0;e<r.length;e++){let t=r[e],i=t.querySelectorAll(".hw-palette__tile, .hw-triplet-chip"),n=!1;for(let e=0;e<i.length;e++)if("none"!==i[e].style.display){n=!0;break}n?(t.removeAttribute("hidden"),t.removeAttribute("data-section-empty")):(t.setAttribute("hidden",""),t.setAttribute("data-section-empty","true"))}}_updatePrimedClasses(){let e=this._editor.getNextAddSymbol(),t=this.element.querySelectorAll(".hw-palette__tile");for(let i=0;i<t.length;i++){let n=t[i],o=n.getAttribute("data-symbol")??"",r=n.getAttribute("data-biotype")??"",s=null!==e&&e.symbol===o&&e.biotype===r,a=(n.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-palette__tile--primed"!==e).join(" ");n.setAttribute("class",s?`${a} hw-palette__tile--primed`:a),n.setAttribute("aria-pressed",s?"true":"false")}}_applyActiveTabClasses(){let e=this.element.querySelectorAll(".hw-palette__tab");for(let t=0;t<e.length;t++){let i=e[t],n=i.getAttribute("data-tab")??"";i.setAttribute("aria-selected",n===this._activeTab?"true":"false")}let t=this.element.querySelectorAll(".hw-palette__pane");for(let e=0;e<t.length;e++){let i=t[e];(i.getAttribute("data-tab")??"")===this._activeTab?i.removeAttribute("hidden"):i.setAttribute("hidden","")}}_localStorage(){if(!this._opts.allowFavorites)return null;let e=this._doc.defaultView;if(null==e)return null;try{return e.localStorage??null}catch{return null}}_resolveInitialTab(e){if(void 0!==e&&Ao.includes(e))return e;let t=this._localStorage();if(null!==t)try{let e=t.getItem(yo);if(null!==e&&Ao.includes(e))return e}catch{}return bo}_persistActiveTab(){let e=this._localStorage();if(null!==e)try{e.setItem(yo,this._activeTab)}catch{}}_loadFavorites(){let e=this._localStorage();if(null!==e){try{let t=e.getItem(_o);if(null!==t&&""!==t){let e=JSON.parse(t),i=this._extractSymbols(e);for(let e of i)this._favorites.add(e);for(let t of this._extractTriplets(e))this._favoriteTriplets.push(t);return}}catch{}try{let t=e.getItem("hwe.palette.favorites");if(null===t||""===t)return;let i=JSON.parse(t);if(Array.isArray(i)){for(let e of i){if("string"!=typeof e)continue;let t=e.indexOf("|"),i=t>=0?e.slice(t+1):e;""!==i&&this._favorites.add(i)}this._saveFavorites()}}catch{}}}_extractSymbols(e){if(Array.isArray(e)){let t=[];for(let i of e)"string"==typeof i&&t.push(i);return t}if(null!==e&&"object"==typeof e){let t=e;if(Array.isArray(t.symbols)){let e=[];for(let i of t.symbols)"string"==typeof i&&e.push(i);return e}}return[]}_extractTriplets(e){if(null===e||"object"!=typeof e)return[];let t=e;if(!Array.isArray(t.triplets))return[];let i=[];for(let e of t.triplets){if(null===e||"object"!=typeof e)continue;let t=e;"string"==typeof t.sugar&&"string"==typeof t.base&&"string"==typeof t.linker&&i.push({sugar:t.sugar,base:t.base,linker:t.linker})}return i}_saveFavorites(){let e=this._localStorage();if(null!==e)try{let t={symbols:Array.from(this._favorites)};this._favoriteTriplets.length>0&&(t.triplets=this._favoriteTriplets.map(e=>({...e}))),e.setItem(_o,JSON.stringify(t))}catch{}}};wo._DEFAULT_TRIPLET_BASES=["A","C","G","U","T"],wo._PALETTE_RDKIT_CACHE_LIMIT=256;var xo=wo,Co='<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round" stroke-linejoin="round">',Eo={new:`${Co}<path d="M13 3H7a2 2 0 0 0-2 2v14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V9z"/><path d="M13 3v6h6"/><line x1="12" y1="12.5" x2="12" y2="17.5"/><line x1="9.5" y1="15" x2="14.5" y2="15"/></svg>`,open:`${Co}<path d="m6 14 1.45-2.9A2 2 0 0 1 9.24 10H20a2 2 0 0 1 1.94 2.5l-1.55 6a2 2 0 0 1-1.94 1.5H4a2 2 0 0 1-2-2V5a2 2 0 0 1 2-2h3.93a2 2 0 0 1 1.66.9l.82 1.2a2 2 0 0 0 1.66.9H18a2 2 0 0 1 2 2v2"/></svg>`,save:`${Co}<rect x="8" y="2" width="8" height="4" rx="1" ry="1"/><path d="M16 4h2a2 2 0 0 1 2 2v14a2 2 0 0 1-2 2H6a2 2 0 0 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15"/><line x1="21" y1="3" x2="14" y2="10"/><line x1="3" y1="21" x2="10" y2="14"/></svg>`,move:`${Co}<polyline points="5 9 2 12 5 15"/><polyline points="9 5 12 2 15 5"/><polyline points="15 19 12 22 9 19"/><polyline points="19 9 22 12 19 15"/><line x1="2" y1="12" x2="22" y2="12"/><line x1="12" y1="2" x2="12" y2="22"/></svg>`,clean:`${Co}<path d="m21.64 3.64-1.28-1.28a1.21 1.21 0 0 0-1.72 0L2.36 18.64a1.21 1.21 0 0 0 0 1.72l1.28 1.28a1.2 1.2 0 0 0 1.72 0L21.64 5.36a1.2 1.2 0 0 0 0-1.72Z"/><path d="m14 7 3 3"/><path d="M5 6v4"/><path d="M19 14v4"/><path d="M10 2v2"/><path d="M7 8H3"/><path d="M21 16h-4"/><path d="M11 3H9"/></svg>`,find:`${Co}<circle cx="11" cy="11" r="8"/><line x1="21" y1="21" x2="16.65" y2="16.65"/></svg>`,theme:`${Co}<circle cx="12" cy="12" r="9"/><path d="M12 3a9 9 0 0 1 0 18z" fill="currentColor" stroke="none"/></svg>`},ko={new:"New — clear the canvas",open:"Open — paste a HELM string",save:"Save — copy HELM string to clipboard",undo:"Undo last action",redo:"Redo last undone action",eraser:"Eraser — click an atom or bond to delete it",select:"Select mode (default)",hbond:"H-Bond mode — drag between two RNA bases to add a Watson-Crick pair","zoom-in":"Zoom in","zoom-out":"Zoom out",fit:"Fit to content — reset zoom and pan",move:"Move/Pan mode — drag the canvas to scroll",clean:"Clean layout — re-run automatic layout",find:"Find / Replace monomer",theme:"Toggle dark / light theme"},Bo=[{id:"new",label:"New",icon:"New"},{id:"open",label:"Open",icon:"Open"},{id:"save",label:"Save",icon:"Save"},{id:"undo",label:"Undo",icon:"↺",shortcut:"Ctrl+Z",separator:!0},{id:"redo",label:"Redo",icon:"↻",shortcut:"Ctrl+Y"},{id:"eraser",label:"Eraser",icon:"Eraser",separator:!0},{id:"select",label:"Select",icon:"Select"},{id:"hbond",label:"H-Bond",icon:"H-Bond"},{id:"zoom-in",label:"Zoom In",icon:"+",shortcut:"Ctrl++",separator:!0},{id:"zoom-out",label:"Zoom Out",icon:"−",shortcut:"Ctrl+−"},{id:"fit",label:"Fit",icon:"Fit",shortcut:"0"},{id:"move",label:"Move",icon:"Move"},{id:"clean",label:"Clean",icon:"Clean",separator:!0},{id:"find",label:"Find",icon:"Find",shortcut:"Ctrl+F"},{id:"theme",label:"Theme",icon:"Theme",separator:!0}],So=class{constructor(e,t,i){this._buttons=new Map,this._unsubs=[],this._destroyed=!1,this._editor=t,this._doc=i?.documentImpl??vn(e);let n=i?.buttons??Bo;this.element=wn(this._doc,"div",{class:"hw-toolbar","data-testid":"toolbar"}),e.appendChild(this.element);for(let e of n){if(!0===e.separator){let e=wn(this._doc,"span",{class:"hw-toolbar__separator"});this.element.appendChild(e)}let t=this._buildButton(e);this.element.appendChild(t),this._buttons.set(e.id,t)}let o=()=>this._refreshHistoryState();this._unsubs.push(t.on("mol:changed",o)),this._unsubs.push(t.on("helm:changed",o)),o(),this._reflectMode(),this._unsubs.push(t.on("option:change",e=>{"mode"===e.key&&this._reflectMode()}))}setButtonEnabled(e,t){let i=this._buttons.get(e);void 0!==i&&(t?i.removeAttribute("disabled"):i.setAttribute("disabled",""))}destroy(){if(!this._destroyed){this._destroyed=!0,this._hideTip();for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_buildButton(e){let t=this._doc.createElement("button");t.setAttribute("class","hw-toolbar__btn"),t.setAttribute("type","button"),t.setAttribute("data-action",e.id),t.setAttribute("data-testid",`toolbar-${e.id}`);let i=ko[e.id]??e.label,n=void 0!==e.shortcut?`${i} (${e.shortcut})`:i;t.setAttribute("data-tooltip",n),t.setAttribute("aria-label",i),t.addEventListener("mouseenter",e=>{let t=e;this._showTip(n,"number"==typeof t.clientX?t.clientX:0,"number"==typeof t.clientY?t.clientY:0)}),t.addEventListener("mouseleave",()=>this._hideTip()),t.addEventListener("click",()=>this._hideTip());let o=Eo[e.id];if(void 0!==o){let e=this._doc.createElement("span");e.setAttribute("class","hw-toolbar__btn-icon"),e.setAttribute("aria-hidden","true"),e.innerHTML=o,t.appendChild(e)}else{let i=e.icon??e.label;t.appendChild(this._doc.createTextNode(i))}return t.addEventListener("click",()=>this._invoke(e.id)),t}_showTip(e,t,i){let n=Cn(this._doc,"toolbar-tooltip","hw-toolbar-tooltip");for(;null!==n.firstChild;)n.removeChild(n.firstChild);n.appendChild(this._doc.createTextNode(e)),kn(n,t,i)}_hideTip(){Bn(this._doc.body.querySelector('[data-testid="toolbar-tooltip"]'))}_invoke(e){let t=!1;this._editor.fire("key:command",{command:e,preventDefault:()=>{t=!0}}),!t&&this._execute(e)}_execute(e){switch(e){case"new":return void this._editor.setHelm("");case"open":{let e=this._doc.defaultView;if(null!=e&&"function"==typeof e.prompt){let t=e.prompt("Enter HELM string");null!==t&&this._editor.setHelm(t)}return}case"save":{let e=this._editor.getHelm();return void this._editor.fire("clipboard:copy",{format:"helm",payload:e})}case"undo":return void this._editor.undo();case"redo":return void this._editor.redo();case"eraser":return this._editor.getSelection().isEmpty?void this._editor.setMode("eraser"):void this._editor.deleteSelection();case"select":case"hbond":case"move":return void this._editor.setMode(e);case"zoom-in":return void this._editor.zoom(1.1,this._molCenterOrUndefined());case"zoom-out":return void this._editor.zoom(1/1.1,this._molCenterOrUndefined());case"fit":return void this._editor.fitToContent();case"clean":return void this._editor.cleanLayout();case"find":return void this._editor.openFindReplace();case"theme":{let e=this._editor,t="function"==typeof e._currentTheme?e._currentTheme():null,i=null!==t&&"dark"===t.name;return void this._editor.setTheme(i?si:ai)}default:return}}_refreshHistoryState(){this.setButtonEnabled("undo",this._editor.canUndo()),this.setButtonEnabled("redo",this._editor.canRedo())}_molCenterOrUndefined(){let e=this._editor.getMol();if(0===e.atoms.length)return;let t=e.atoms[0].p.x,i=t,n=e.atoms[0].p.y,o=n;for(let r=1;r<e.atoms.length;r++){let s=e.atoms[r].p;s.x<t&&(t=s.x),s.x>i&&(i=s.x),s.y<n&&(n=s.y),s.y>o&&(o=s.y)}return{x:(t+i)/2,y:(n+o)/2}}_reflectMode(){let e=this._editor.getMode();for(let t of["select","eraser","hbond","move"]){let i=this._buttons.get(t);if(void 0===i)continue;let n=(i.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-toolbar__btn--active"!==e).join(" ");i.setAttribute("class",t===e?`${n} hw-toolbar__btn--active`:n)}}},Mo=class{constructor(e,t,i){this._unsubs=[],this._destroyed=!1,this._editor=t,this._doc=i?.documentImpl??vn(e),this._content=wn(this._doc,"pre",{class:"hw-pane__content hw-pane__sequence","data-testid":"sequence-pane-content"}),this.element=wn(this._doc,"div",{class:"hw-pane hw-pane--sequence","data-testid":"pane-sequence"},[this._content]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on("helm:changed",()=>this.refresh())),this._unsubs.push(t.on("mol:changed",()=>this.refresh()))}refresh(){if(this._destroyed)return;let e=this._compute();for(;null!==this._content.firstChild;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e))}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_compute(){let e,t=this._editor.getMol(),i=[];for(let n of t.atoms){let t=n.bio.chainId;void 0!==e&&t!==e&&i.push("|"),e=t;let o=n.monomer?.naturalAnalog;i.push(void 0!==o&&""!==o?o:n.symbol)}return i.join("")}},To=class{constructor(e,t,i){this._unsubs=[],this._destroyed=!1,this._suppressNext=!1,this._editor=t,this._doc=i?.documentImpl??vn(e),this._input=wn(this._doc,"div",{class:"hw-pane__content hw-pane__notation",contenteditable:"true",spellcheck:"false","data-testid":"notation-pane-content"}),this._error=wn(this._doc,"div",{class:"hw-pane__error","data-testid":"notation-pane-error"}),this.element=wn(this._doc,"div",{class:"hw-pane hw-pane--notation","data-testid":"pane-helm"},[this._input,this._error]),e.appendChild(this.element),this.refresh(),this._input.addEventListener("blur",()=>this._commit()),this._input.addEventListener("keydown",e=>{"Enter"===e.key&&(e.preventDefault(),e.stopPropagation(),e.stopImmediatePropagation(),this._commit())}),this._unsubs.push(t.on("helm:changed",()=>{this._suppressNext?this._suppressNext=!1:this.refresh()})),this._unsubs.push(t.on("mol:changed",()=>this.refresh()))}refresh(){if(this._destroyed)return;let e=this._editor.getHelm();for(;null!==this._input.firstChild;)this._input.removeChild(this._input.firstChild);this._input.appendChild(this._doc.createTextNode(e)),this._clearError()}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_commit(){if(this._destroyed)return;let e=(this._input.textContent??"").trim();if(e===this._editor.getHelm())return void this._clearError();let t=this._editor.getService().validate(e).filter(e=>"error"===e.severity);t.length>0?this._showError(t.map(e=>e.message).join("; ")):(this._clearError(),this._suppressNext=!0,this._editor.setHelm(e))}_showError(e){for(;null!==this._error.firstChild;)this._error.removeChild(this._error.firstChild);this._error.appendChild(this._doc.createTextNode(e)),this._error.setAttribute("class","hw-pane__error hw-pane__error--visible")}_clearError(){for(;null!==this._error.firstChild;)this._error.removeChild(this._error.firstChild);this._error.setAttribute("class","hw-pane__error")}},Io=class{constructor(e,t,i){this._unsubs=[],this._destroyed=!1,this._editor=t,this._doc=i?.documentImpl??vn(e),this._body=wn(this._doc,"div",{class:"hw-pane__content hw-pane__properties","data-testid":"properties-pane-content"}),this.element=wn(this._doc,"div",{class:"hw-pane hw-pane--properties","data-testid":"pane-properties"},[this._body]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on("helm:changed",()=>this.refresh())),this._unsubs.push(t.on("mol:changed",()=>this.refresh()))}refresh(){if(this._destroyed)return;for(;null!==this._body.firstChild;)this._body.removeChild(this._body.firstChild);let e=this._editor.getHelm();if(e.length>1e3)return void this._body.appendChild(wn(this._doc,"div",{class:"hw-pane__placeholder"},["(too long)"]));let t=this._editor.getService(),i="",n=0,o=0;try{let o=t.getFormula(e);i=function(e){let t=Array.from(e.keys()).sort((e,t)=>e===t?0:"C"===e?-1:"C"===t?1:"H"===e?-1:"H"===t?1:e.localeCompare(t)),i="";for(let n of t){let t=e.get(n);void 0===t||0===t||(i+=1===t?n:`${n}${t}`)}return""===i?"—":i}(o.elements),n=o.mw}catch{i="—"}try{n=t.getMolWeight(e)}catch{}try{o=t.getExtinctionCoefficient(e)}catch{}this._body.appendChild(this._makeRow("Formula",i,"formula")),this._body.appendChild(this._makeRow("Molecular Weight",0===n?"—":n.toFixed(2),"mw")),this._body.appendChild(this._makeRow("Extinction Coefficient",0===o?"—":o.toFixed(0),"extinction"))}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_makeRow(e,t,i){let n=wn(this._doc,"span",{class:"hw-pane__prop-label"},[e]),o=wn(this._doc,"span",{class:"hw-pane__prop-value","data-testid":`properties-${i}`},[t]);return wn(this._doc,"div",{class:"hw-pane__prop-row"},[n,o])}},Lo=class{constructor(e,t,i){this._unsubs=[],this._destroyed=!1,this._refreshToken=0,this._editor=t,this._doc=i?.documentImpl??vn(e),this._content=wn(this._doc,"pre",{class:"hw-pane__content hw-pane__atomic","data-testid":"atomic-pane-content"}),this.element=wn(this._doc,"div",{class:"hw-pane hw-pane--atomic","data-testid":"pane-atomic"},[this._content]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on("helm:changed",()=>{this.refresh()}))}async refresh(){if(this._destroyed)return;let e=++this._refreshToken,t=this._editor.getHelm(),i=this._editor.getService();if(i.hasAtomicMolfileProvider())try{let n=await i.getAtomicMolfile(t);if(this._destroyed||e!==this._refreshToken)return;this._render(n)}catch(t){if(this._destroyed||e!==this._refreshToken)return;let i=t instanceof Error?t.message:String(t);this._render(`Atomic structure unavailable: ${i}`)}else this._render("Atomic structure unavailable")}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_render(e){for(;null!==this._content.firstChild;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e))}};function $o(e){return e.toLowerCase().replace(/[^a-z0-9]+/g,"-").replace(/^-|-$/g,"")}var Po=class{constructor(e,t,i,n,o){this._unsubs=[],this._destroyed=!1,this._active=!1,this._dirty=!0,this._refreshToken=0,this._editor=t,this._provider=n,this.name=i,this._doc=o?.documentImpl??vn(e);let r=$o(i);this._content=wn(this._doc,"div",{class:"hw-pane__content hw-pane__extra","data-testid":`extra-pane-content-${r}`}),this.element=wn(this._doc,"div",{class:"hw-pane hw-pane--extra","data-testid":`pane-extra-${r}`},[this._content]),e.appendChild(this.element),this._unsubs.push(t.on("helm:changed",()=>{this._dirty=!0,this._active&&this.refresh()}))}setActive(e){this._active=e,e&&this._dirty&&this.refresh()}async refresh(){if(this._destroyed)return;let e=++this._refreshToken;this._dirty=!1;let t=this._editor.getHelm();try{let i=await this._provider(t);if(this._destroyed||e!==this._refreshToken)return;this._mount(i)}catch(t){if(this._destroyed||e!==this._refreshToken)return;let i=t instanceof Error?t.message:String(t);this._renderText(`Pane "${this.name}" failed: ${i}`)}}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_mount(e){for(;null!==this._content.firstChild;)this._content.removeChild(this._content.firstChild);this._content.appendChild(e)}_renderText(e){for(;null!==this._content.firstChild;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e))}};function Ro(e){return"extra:"+e}var Ho=[{id:"sequence",label:"Sequence"},{id:"helm",label:"HELM"},{id:"properties",label:"Properties"},{id:"atomic",label:"Atomic Structure"}],No=class{constructor(e,t){this._paneByName=new Map,this._tabsByName=new Map,this._unsubs=[],this._activePane="helm",this._destroyed=!1,this._statusModeNode=null,this._statusMessageNode=null,this._statusMessageTimeout=null,this._host=e,this._doc=t.documentImpl??vn(e);let i="dark"===(t.theme??si).name?"hw-app hw-app--dark":"hw-app";this.element=wn(this._doc,"div",{class:i,"data-testid":"app-root"}),this._toolbarHost=wn(this._doc,"div",{class:"hw-app__toolbar"}),this._paletteHost=wn(this._doc,"div",{class:"hw-app__palette"}),this._canvasHost=wn(this._doc,"div",{class:"hw-app__canvas","data-testid":"canvas-host"});let n=wn(this._doc,"div",{class:"hw-app__main"},[this._paletteHost,this._canvasHost]);this._tabsHost=wn(this._doc,"div",{class:"hw-app__tabs",role:"tablist"}),this._paneBody=wn(this._doc,"div",{class:"hw-app__pane-body"});let o=wn(this._doc,"div",{class:"hw-app__panes"},[this._tabsHost,this._paneBody]);this.element.appendChild(this._toolbarHost),this.element.appendChild(n),this.element.appendChild(o),e.appendChild(this.element);let r={service:t.service};void 0!==t.initialHelm&&(r.initialHelm=t.initialHelm),void 0!==t.width&&(r.width=t.width),void 0!==t.height&&(r.height=t.height),this.canvas=new io(this._canvasHost,r),void 0!==t.theme&&this.canvas.setTheme(t.theme);let s={documentImpl:this._doc};void 0!==t.toolbarButtons&&(s.buttons=t.toolbarButtons),this.toolbar=new So(this._toolbarHost,this.canvas,s),this.palette=new xo(this._paletteHost,this.canvas,{documentImpl:this._doc,...t.paletteOptions}),this.sequencePane=new Mo(this._paneBody,this.canvas,{documentImpl:this._doc}),this.notationPane=new To(this._paneBody,this.canvas,{documentImpl:this._doc}),this.propertiesPane=new Io(this._paneBody,this.canvas,{documentImpl:this._doc}),t.service.hasAtomicMolfileProvider()?this.atomicStructurePane=new Lo(this._paneBody,this.canvas,{documentImpl:this._doc}):this.atomicStructurePane=null,this._paneByName.set("sequence",this.sequencePane.element),this._paneByName.set("helm",this.notationPane.element),this._paneByName.set("properties",this.propertiesPane.element),null!==this.atomicStructurePane&&this._paneByName.set("atomic",this.atomicStructurePane.element);let a=[];for(let[e,i]of t.service.getExtraPanes()){let t=new Po(this._paneBody,this.canvas,e,i,{documentImpl:this._doc});a.push(t),this._paneByName.set(Ro(e),t.element)}this.extraPanes=a;let l=this._resolveVisiblePanes(t),h=[];for(let e of l){let t=Ho.find(t=>t.id===e);void 0!==t&&h.push({id:t.id,label:t.label,testid:`tab-${t.id}`})}for(let e of a)h.push({id:Ro(e.name),label:e.name,testid:`tab-extra-${$o(e.name)}`});for(let{id:e,label:t,testid:i}of h){let n=this._doc.createElement("button");n.setAttribute("type","button"),n.setAttribute("class","hw-app__tab"),n.setAttribute("role","tab"),n.setAttribute("data-pane",e),n.setAttribute("data-testid",i),n.appendChild(this._doc.createTextNode(t)),n.addEventListener("click",()=>this.activatePane(e)),this._tabsHost.appendChild(n),this._tabsByName.set(e,n)}let d=l.includes("helm")?"helm":l[0]??"helm";this.activatePane(d),this._unsubs.push(this.canvas.on("theme:change",e=>this._applyTheme(e.theme))),this._buildStatusBar(),this._applyMode(this.canvas.getMode()),this._unsubs.push(this.canvas.on("option:change",e=>{"mode"===e.key&&this._applyMode(e.newValue),"nextAdd"===e.key&&this._refreshStatus()})),this._unsubs.push(this.canvas.on("mol:changed",()=>this._refreshStatus())),this._unsubs.push(this.canvas.on("helm:changed",()=>this._refreshStatus())),this._unsubs.push(this.canvas.on("editor:status",e=>{this._showStatusMessage(e.message,e.severity,e.durationMs)})),this._unsubs.push(this.canvas.on("monomer:contextmenu",e=>{e.preventDefault(),this.canvas.openAtomProps(e.atom)})),this._unsubs.push(this.canvas.on("bond:contextmenu",e=>{e.preventDefault(),this.canvas.openBondProps(e.bond)})),this._onDocKeydown=e=>this._handleEscape(e),this._doc.addEventListener("keydown",this._onDocKeydown,!0)}_handleEscape(e){let t=e;"Escape"===t.key&&(Sn(this._doc),$n.closeTopmost()&&(t.stopImmediatePropagation?.(),t.preventDefault?.()))}_buildStatusBar(){let e=wn(this._doc,"div",{class:"hw-status-bar","data-testid":"status-bar"}),t=wn(this._doc,"span",{class:"hw-status-bar__mode","data-testid":"status-mode"}),i=wn(this._doc,"span",{class:"hw-status-bar__message","data-testid":"status-message",role:"status","aria-live":"polite"});e.appendChild(t),e.appendChild(i),this._canvasHost.appendChild(e),this._statusModeNode=t,this._statusMessageNode=i,this._refreshStatus()}_refreshStatus(){let e=this._statusModeNode;if(null===e)return;let t=this.canvas.getMode(),i=this.canvas.getNextAddSymbol();for(;null!==e.firstChild;)e.removeChild(e.firstChild);if(null===i)return void e.appendChild(this._doc.createTextNode(`Mode: ${t} | Next add: none`));e.appendChild(this._doc.createTextNode(`Mode: ${t} | Next add: `));let n=wn(this._doc,"span",{class:"hw-status-bar__next-add-symbol","data-testid":"status-next-add-symbol"},[i.symbol]);e.appendChild(n);let o=wn(this._doc,"button",{type:"button",class:"hw-status-bar__next-add-clear","data-testid":"status-next-add-clear","aria-label":"Clear next-add monomer",title:"Clear (Esc)"},["×"]);o.addEventListener("click",e=>{e.preventDefault(),e.stopPropagation(),this.canvas.setNextAddSymbol(null)}),e.appendChild(o)}_showStatusMessage(e,t,i){let n=this._statusMessageNode;if(null!==n){for(null!==this._statusMessageTimeout&&(clearTimeout(this._statusMessageTimeout),this._statusMessageTimeout=null);null!==n.firstChild;)n.removeChild(n.firstChild);n.appendChild(this._doc.createTextNode(e)),n.setAttribute("data-severity",t),i>0&&(this._statusMessageTimeout=setTimeout(()=>{let e=this._statusMessageNode;if(null!==e){for(;null!==e.firstChild;)e.removeChild(e.firstChild);e.removeAttribute("data-severity"),this._statusMessageTimeout=null}},i))}}_applyMode(e){let t=this._canvasHost.querySelector(".hw-editor-view");if(null===t)return;let i=(t.getAttribute("class")??"").split(/\s+/).filter(e=>!e.startsWith("hw-editor-view--")).join(" ");t.setAttribute("class",`${i} hw-editor-view--${e}`.trim()),this._refreshStatus()}setHelm(e){this.canvas.setHelm(e)}getHelm(){return this.canvas.getHelm()}on(e,t){return this.canvas.on(e,t)}activatePane(e){if(this._paneByName.has(e)||this._tabsByName.has(e)){this._activePane=e;for(let[t,i]of this._paneByName.entries())i.style.display=t===e?"":"none";for(let[t,i]of this._tabsByName.entries()){let n=(i.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-app__tab--active"!==e).join(" ");i.setAttribute("class",t===e?`${n} hw-app__tab--active`:n)}for(let e of this.extraPanes)e.setActive(this._activePane===Ro(e.name))}}getActivePane(){return this._activePane}destroy(){if(!this._destroyed){this._destroyed=!0,null!==this._statusMessageTimeout&&(clearTimeout(this._statusMessageTimeout),this._statusMessageTimeout=null),this._doc.removeEventListener("keydown",this._onDocKeydown,!0);for(let e of this._unsubs)e();for(let e of this.extraPanes)e.destroy();null!==this.atomicStructurePane&&this.atomicStructurePane.destroy(),this.propertiesPane.destroy(),this.notationPane.destroy(),this.sequencePane.destroy(),this.palette.destroy(),this.toolbar.destroy(),this.canvas.destroy(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element),this._host}}_resolveVisiblePanes(e){let t=e.service.hasAtomicMolfileProvider(),i=e.visiblePanes??["sequence","helm","properties","atomic"];return t||(i=i.filter(e=>"atomic"!==e)),i}_applyTheme(e){let t="dark"===e.name,i=(this.element.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-app--dark"!==e).join(" ");this.element.setAttribute("class",t?`${i} hw-app--dark`:i)}},Do=class{constructor(e){this.T="ATOM",this.selected=e.selected,this.highlighted=e.highlighted,this.p={x:e.p.x,y:e.p.y},this.elem=e.symbol,this.bio={type:e.biotype,continuousId:e.bio.continuousId,chainId:e.bio.chainId,positionInChain:e.bio.positionInChain,...void 0!==e.bio.annotation?{annotation:e.bio.annotation}:{},...void 0!==e.bio.blobtype?{blobtype:e.bio.blobtype}:{},...void 0!==e.bio.ambiguity?{ambiguity:e.bio.ambiguity}:{},id:e.id},void 0!==e.inlineSource&&(this.inlineSource=e.inlineSource)}biotype(){return this.bio.type}},Fo=class{constructor(e,t,i){this.a1=t,this.a2=i,this.r1=Oo(e.r1),this.r2=Oo(e.r2),this.kind=e.kind}};function Oo(e){switch(e.kind){case"numeric":case"positional":return e.r;default:return 0}}function zo(e){let t=[],i=new Map;for(let n of e.atoms){let e=new Do(n);t.push(e),i.set(n.id,e)}let n=[];for(let t of e.bonds){let e=i.get(t.a1.id),o=i.get(t.a2.id);void 0===e||void 0===o||n.push(new Fo(t,e,o))}return{atoms:t,bonds:n,clone:t=>zo(e),_internalMol:e}}var Go=class{constructor(e,t,i){this._laidMol=null,this._currentHelm="",this._drawOptions={fontsize:14},this._noDraw=!1,this._svgEl=null,this.host=e,this._service=t,this._doc=i?.documentImpl??vn(e),this._width=i?.width??400,this._height=i?.height??100,this._mol=Y(),this._molView=zo(this._mol),this.editor=this._buildEditor()}resizeEditor(e,t){this._width=e,this._height=t,this._redraw()}_buildEditor(){let e=this,t={get noDraw(){return e._noDraw},set noDraw(t){e._noDraw=t},get jsd(){return e.editor}};return{get div(){return e.host},get m(){return e._molView},set m(t){e._molView=t},get helm(){return t},get options(){return{width:e._width,height:e._height}},setData(t,i){if("helm"!==i)throw new Error(`LegacyEditorWrapper: only 'helm' format supported (got '${i}').`);e._setHelm(t)},setHelm(t){e._setHelm(t)},setMol(t){e._mol=t._internalMol,e._molView=e._buildView(e._mol),e._currentHelm=e._service.serialize(e._mol),e._redraw()},getHelm:t=>e._currentHelm,getMolfile:()=>Ji(e._mol),resize(t,i){e._width=t,e._height=i,e._redraw()},setSize(t,i){e._width=t,e._height=i,e._redraw()},redraw(){e._redraw()},reset(){e._mol=Y(),e._laidMol=null,e._molView=zo(e._mol),e._currentHelm="",e._removeSvg()},getFormula:t=>function(e){let t=e=>{let t=qo.indexOf(e);return-1===t?qo.length:t},i=[...e.elements.keys()].sort((e,i)=>{let n=t(e),o=t(i);return n!==o?n-o:e<i?-1:e>i?1:0}),n=[];for(let t of i){let i=e.elements.get(t);n.push(1===i?t:`${t}${i}`)}return n.join("")}(Fi(e._mol)),getMolWeight:()=>Yi(e._mol),getExtinctionCoefficient:()=>Ki(e._mol),getDrawOptions:()=>e._drawOptions}}_setHelm(e){this._currentHelm=e;let t=this._service.parse(e,{mode:"lenient",resolveMonomers:!0});this._mol=t.mol,this._molView=this._buildView(this._mol),this._redraw()}_buildView(e){return this._laidMol=this._noDraw?null:Ut(e),zo(this._laidMol??e)}_redraw(){if(this._noDraw)return void this._removeSvg();if(""===this._currentHelm||null===this._laidMol)return void this._removeSvg();let e=new Set,t=new Set;for(let i of this._molView.atoms){let n=i.bio.id;void 0!==n&&(i.selected&&e.add(n),i.highlighted&&t.add(n))}let i=this._service.renderMolResult(this._laidMol,{width:this._width,height:this._height,maxScale:1/0,showIds:!0,selectedAtomIds:e,highlightedAtomIds:t});this._bakeViewToSurface(i.bbox,i.drawBox),this._mountSvg(i.svg)}_bakeViewToSurface(e,t){if(null===this._laidMol)return;let i=t.scale,n=t.x-e.x*i,o=t.y-e.y*i,r=this._laidMol.atoms,s=this._molView.atoms,a=Math.min(r.length,s.length);for(let e=0;e<a;e++){let t=r[e].p,a=s[e].p;a.x=t.x*i+n,a.y=t.y*i+o}}_mountSvg(e){this._removeSvg();let t=function(e,t,i,n){let o=function(e,t){let i=globalThis.DOMParser;if(void 0===i)return null;try{let n=(new i).parseFromString(t,"image/svg+xml").documentElement;return null==n?null:e.importNode(n,!0)}catch{return null}}(e,t);if(null!==o)return o;let r=e.createElementNS("http://www.w3.org/2000/svg","svg");return r.setAttribute("width",String(i)),r.setAttribute("height",String(n)),r}(this._doc,e,this._width,this._height);t.setAttribute("pointer-events","none"),null!==this.host.firstChild?this.host.insertBefore(t,this.host.firstChild):this.host.appendChild(t),this._svgEl=t}_removeSvg(){null!==this._svgEl&&null!==this._svgEl.parentNode&&this._svgEl.parentNode.removeChild(this._svgEl),this._svgEl=null}},qo=["C","H","N","O","S","P"],jo=class{constructor(e){this._width=0,this._height=0,this._doc=e}resize(e,t){this._width=e,this._height=t}select(){}dblclick(){}createMonomerDiv(e,t,i){let n=wn(this._doc,"div",{"data-monomer":t,"data-biotype":i,"data-testid":`legacy-mex-monomer-${t}`});return e.appendChild(n),n}getSize(){return{width:this._width,height:this._height}}},Vo=class{constructor(e,t,i){this.toolbarheight=32,this._drawOptions={fontsize:14},this._unsubs=[],this._destroyed=!1,this._host=e,this._service=t,this._doc=i?.documentImpl??vn(e),this._width=i?.width??800,this._height=i?.height??400;let n={service:t};void 0!==i?.initialHelm&&(n.initialHelm=i.initialHelm),void 0!==i?.documentImpl&&(n.documentImpl=i.documentImpl),void 0!==i?.width&&(n.width=i.width),void 0!==i?.height&&(n.height=i.height),this._app=new No(e,n),this.sequence=this._app.sequencePane.element,this.notation=this._app.notationPane.element,this.properties={parent:this._app.propertiesPane.element},this._structureviewHost=wn(this._doc,"div",{class:"hwe-legacy-app__structureview","data-testid":"legacy-app-structureview"}),this._structureviewWrapper=new Go(this._structureviewHost,t,{documentImpl:this._doc}),this.structureview=this._structureviewWrapper,this.mex=new jo(this._doc),this._editorFacade=this._buildEditorFacade();let o=this._editorFacade;this.canvas={get host(){return o.div},get editor(){return o},get helm(){return o.helm},resizeEditor:(e,t)=>{this._resize(e,t)},getHelm:e=>o.getHelm(e),setHelm:e=>{o.setHelm(e)}};let r=()=>{this._structureviewWrapper.editor.setHelm(this._app.getHelm())};this._unsubs.push(this._app.canvas.on("helm:changed",r)),void 0!==i?.initialHelm&&i.initialHelm.length>0&&r()}get editorApp(){return this._app}_buildEditorFacade(){let e=this,t=this._app,i={noDraw:!1,get jsd(){return e._editorFacade}};return{get div(){return t.element},get m(){return e._currentMolView()},set m(e){null!=e&&void 0!==e._internalMol&&t.canvas.setMol(e._internalMol)},get helm(){return i},get options(){return{width:e._width,height:e._height}},setData(e,i){if("helm"!==i)throw new Error(`LegacyAppWrapper: only 'helm' format supported (got '${i}').`);t.setHelm(e)},setHelm(e){t.setHelm(e)},setMol(e){t.canvas.setMol(e._internalMol)},getHelm:e=>t.getHelm(),getMolfile:()=>e._service.getMolfile(t.getHelm()),resize(t,i){e._resize(t,i)},setSize(t,i){e._resize(t,i)},redraw(){t.canvas.redraw()},reset(){t.setHelm("")},getFormula:e=>function(e){let t=[];for(let[i,n]of e.elements.entries())t.push(1===n?i:`${i}${n}`);return t.join("")}(Fi(t.canvas.getMol())),getMolWeight:()=>Yi(t.canvas.getMol()),getExtinctionCoefficient:()=>Ki(t.canvas.getMol()),getDrawOptions:()=>e._drawOptions}}_currentMolView(){let e=zo(this._app.canvas.getMol()),t=this._app.canvas.getSelection();if(!t.isEmpty)for(let i of e.atoms){let e=i.bio.id;"number"==typeof e&&(i.selected=t.atoms.has(e))}return e}_resize(e,t){this._width=e,this._height=t,this._app.canvas.resize(e,t)}calculateSizes(){let e=Yo(this._host.clientWidth,this._width),t=Yo(this._host.clientHeight,this._height);this._resize(e,Math.max(50,t-this.toolbarheight))}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();this._unsubs.length=0,this._app.destroy()}}};function Yo(e,t){return"number"!=typeof e||isNaN(e)||e<=0?t:e}var Wo=class{constructor(e,t,i){this._tooltip=null,this._destroyed=!1,this.name=e,this._service=t;let n=i?.documentImpl??globalThis.document??null;if(null===n)throw new Error("LegacyInputWrapper: no Document available.");this._doc=n,this._host=wn(this._doc,"div",{class:"hwe-legacy-input","data-testid":"legacy-input-host"}),this.viewer=new Go(this._host,t,{width:i?.editorOptions?.width??240,height:i?.editorOptions?.height??80,documentImpl:this._doc})}get value(){return this.viewer.editor.getHelm()}set value(e){this._ensureLive(),this.viewer.editor.setHelm(e)}get molValue(){return this.viewer.editor.m}set molValue(e){this._ensureLive(),this.viewer.editor.setMol(e)}redraw(){this._ensureLive(),this.viewer.editor.redraw()}showTooltip(e,t){this._ensureLive(),null!==this._tooltip&&null!==this._tooltip.parentNode&&this._tooltip.parentNode.removeChild(this._tooltip);let i=wn(this._doc,"div",{class:"hwe-legacy-input__tooltip","data-testid":"legacy-input-tooltip",style:`position: absolute; left: ${t.p.x}px; top: ${t.p.y}px;`});"string"==typeof e?i.appendChild(this._doc.createTextNode(e)):i.appendChild(e),this._host.appendChild(i),this._tooltip=i}destroy(){this._destroyed||(this._destroyed=!0,null!==this._tooltip&&null!==this._tooltip.parentNode&&this._tooltip.parentNode.removeChild(this._tooltip),null!==this._host.parentNode&&this._host.parentNode.removeChild(this._host))}getHost(){return this._host}getTooltip(){return this._tooltip}_ensureLive(){if(this._destroyed)throw new Error("LegacyInputWrapper: this instance has been destroyed.");this._service}},Uo=/^R([1-9][0-9]*)$/,Ko=new Set([ne.PEPTIDE,ne.RNA,ne.CHEM,ne.BLOB]),Xo=new Set(["Backbone","Branch","Terminal","Undefined"]);function Qo(e){if("string"!=typeof e.symbol||0===e.symbol.length||"string"!=typeof e.molfile||!Ko.has(e.polymerType)||!Xo.has(e.monomerType))return null;let t=[];for(let i of e.rgroups??[]){if("string"!=typeof i.label||!Uo.test(i.label))continue;let e={label:i.label,capGroupName:"string"==typeof i.capGroupName?i.capGroupName:"",capGroupSMILES:Le(i)??""};"string"==typeof i.alternateId&&(e.alternateId=i.alternateId),t.push(e)}let i={symbol:e.symbol,molfile:e.molfile,polymerType:e.polymerType,monomerType:e.monomerType,rgroups:t};return"string"==typeof e.name&&(i.name=e.name),"string"==typeof e.smiles&&(i.smiles=e.smiles),"string"==typeof e.naturalAnalog&&(i.naturalAnalog=e.naturalAnalog),void 0!==e.meta&&null!==e.meta&&(i.meta={...e.meta}),"string"==typeof e.author&&(i.author=e.author),void 0!==e.createDate&&(i.createDate=e.createDate),"number"==typeof e.id&&(i.id=e.id),i}function Zo(e,t,i){if(e===ne.PEPTIDE)return X;if(e===ne.CHEM)return ee;if(e===ne.BLOB)return te;if(e===ne.RNA){if("Branch"===t)return Z;if("Backbone"===t)return"P"===i||"p"===i?J:Q}return X}var Jo=class{constructor(e,t){this._cache=new Map,this._polymerTypesCache=null,this._version=0,this._base=e,this.source=t??("string"==typeof e.source?e.source:"datagrok-bridge"),this.onChanged=new ae,this._unsub=function(e,t){let i=e.subscribe(t);return()=>{null!=i&&"function"==typeof i.unsubscribe&&i.unsubscribe()}}(e.onChanged,()=>{this._cache.clear(),this._polymerTypesCache=null,this._version+=1,this.onChanged.next({type:"reload"})})}get version(){return this._version}get isEmpty(){return"boolean"==typeof this._base.isEmpty?this._base.isEmpty:0===this.getPolymerTypes().length}getMonomer(e,t){let i=`${e}|${t}`;if(this._cache.has(i))return this._cache.get(i)??null;let n=this._base.getMonomer(e,t),o=null==n?null:this._enrichColors(Qo(n));return this._cache.set(i,o),o}_enrichColors(e){if(null===e)return null;let t=this._base;if("function"!=typeof t.getMonomerColors)return e;let i=Zo(e.polymerType,e.monomerType,e.naturalAnalog),n=null;try{n=t.getMonomerColors(i,e.symbol)}catch{n=null}if(null==n)return e;let o=n.backgroundcolor,r=n.textcolor,s=n.linecolor;if("string"!=typeof o||"string"!=typeof r||"string"!=typeof s)return e;let a={...e.meta??{},colors:{...e.meta?.colors??{},default:{line:s,text:r,background:o}}};return{...e,meta:a}}registerInlineSmilesMonomer(e,t){let i=this._base;var n;"function"==typeof i.getWebEditorMonomer&&i.getWebEditorMonomer((n=e)===ne.PEPTIDE?X:n===ne.RNA?Q:n===ne.CHEM?ee:n===ne.BLOB?te:X,t);let o=i.getMonomer(e,t),r=null==o?null:this._enrichColors(Qo(o));if(null===r)throw new Error(`BridgedMonomerLib: could not register inline SMILES monomer '${t}'`);return this._cache.set(`${e}|${t}`,r),this._cache.set(`${e}|${r.symbol}`,r),r}getMonomerSet(e){let t=new Map;for(let i of this.getPolymerTypes())for(let n of this.getMonomerSymbolsByType(i)){let o=this.getMonomer(i,n);null!==o&&Zo(o.polymerType,o.monomerType,o.naturalAnalog)===e&&t.set(n,o)}return t}getMonomerSymbolsByType(e){return this._base.getMonomerSymbolsByType(e)}getByNaturalAnalog(e,t){let i=[];for(let n of this.getMonomerSymbolsByType(e)){let o=this.getMonomer(e,n);null!==o&&o.naturalAnalog===t&&i.push(o)}return i}getPolymerTypes(){if(null!==this._polymerTypesCache)return this._polymerTypesCache;let e=[],t="function"==typeof this._base.getPolymerTypes?this._base.getPolymerTypes():Object.values(ne);for(let i of t){if(!Ko.has(i))continue;let t=this._base.getMonomerSymbolsByType(i);Array.isArray(t)&&t.length>0&&e.push(i)}return this._polymerTypesCache=e,e}getColors(e,t){let i="dark"===t?Te:Se;return Ie(e,null===e?X:Zo(e.polymerType,e.monomerType,e.naturalAnalog),i)}addMonomer(e){throw new Error("BridgedMonomerLib: mutation is not supported on a Datagrok-bridged library.")}removeMonomer(e,t){return!1}merge(e){throw new Error("BridgedMonomerLib: mutation is not supported on a Datagrok-bridged library.")}toJSON(){let e=[];for(let t of this.getPolymerTypes())for(let i of this.getMonomerSymbolsByType(t)){let n=this.getMonomer(t,i);null!==n&&e.push(n)}return e}destroy(){this._unsub(),this.onChanged.complete(),this._cache.clear()}};function er(e,t){return new Jo(e,t)}var tr=class e{constructor(e){if(this._overriddenFuncs=null,this._originalFuncs=null,this._molfilesEditor=null,this._molfilesEditorHost=null,this._molfilesGcTimer=null,void 0===e.service||null===e.service)throw new TypeError("HelmHelperAdapter: options.service is required");this._service=e.service,this.seqHelper=e.seqHelper??null,this._logger=e.logger??new F,this._bridge=e.monomerLibBridge??(e=>er(e)),this._doc=e.documentImpl??rr()}get service(){return this._service}createHelmInput(e,t){let i={...t};return void 0===i.documentImpl&&null!==this._doc&&(i.documentImpl=this._doc),new Wo(e,this._service,i)}createHelmWebEditor(e,t){let i=e??this._createDetachedHost();return new Go(i,this._service,{...void 0!==t?.width?{width:t.width}:{},...void 0!==t?.height?{height:t.height}:{},...null!==this._doc?{documentImpl:this._doc}:{}})}createWebEditorApp(e,t){return new Vo(e,this._service,{...void 0!==t?{initialHelm:t}:{},...null!==this._doc?{documentImpl:this._doc}:{}})}get originalMonomersFuncs(){return this._originalFuncs}buildMonomersFuncsFromLib(e){let t=this._bridge(e),i=e;return{getMonomer:function(e,n){if("function"==typeof i.getWebEditorMonomer){let t=i.getWebEditorMonomer(e,n);if(null!=t)return t}let{biotype:o,symbol:r}=sr(e,n);if(null===r)return null;let s=(h=r).length>=2&&"["===h.charAt(0)&&"]"===h.charAt(h.length-1)?h.slice(1,h.length-1):h,a=ar(o),l=t.getMonomer(a,s);var h;return null===l?null:lr(l,s)},getMonomerSet:function(e){let{biotype:i}=sr(e,void 0),n=ar(i),o={};for(let e of t.getMonomerSymbolsByType(n)){let i=t.getMonomer(n,e);null!==i&&(o[e]=lr(i,e))}return o}}}overrideMonomersFuncs(e){let t=this._overriddenFuncs;return null===this._originalFuncs&&(this._originalFuncs=t??this._defaultFuncs()),this._overriddenFuncs=e,t??this._originalFuncs}revertOriginalMonomersFuncs(){let e=this._originalFuncs??this._defaultFuncs(),t=this._overriddenFuncs??e;return this._overriddenFuncs=e,this._originalFuncs=null,t}getHoveredAtom(e,t,i,n){let o=new bn(i._internalMol,si).test({x:e,y:t});if(null===o||void 0===o.atom)return null;for(let e of i.atoms)if(e.bio.id===o.atom.id||void 0===e.bio.id&&e.bio.continuousId===o.atom.bio.continuousId)return e;return null}getMolfiles(e){let t=this._ensureMolfilesEditor();t.editor.helm.noDraw=!0;try{let i=[];for(let n of e)"string"==typeof n&&0!==n.length?(t.editor.setHelm(n),i.push(t.editor.getMolfile())):i.push("");return i}finally{t.editor.helm.noDraw=!1,this._scheduleMolfilesEditorGc()}}parse(e,t){return zo(Ut(this._service.parse(e,{mode:"lenient",resolveMonomers:!1}).mol))}removeGaps(e){let t;try{t=this._service.removeGaps(e)}catch(e){throw e instanceof N&&void 0===e.type&&(e.type="HelmNotSupportedError"),e}let i=function(e,t){try{let i=e.parse(t,{mode:"lenient",resolveMonomers:!1});for(let e of i.mol.atoms)if("*"===e.symbol)return!0;return!1}catch{return!1}}(this._service,e);return{srcHelm:t.srcHelm,resHelm:t.resHelm,monomerMap:i?new Map(t.monomerMap):null}}destroy(){null!==this._molfilesGcTimer&&(clearTimeout(this._molfilesGcTimer),this._molfilesGcTimer=null),this._removeMolfilesEditorNow()}_defaultFuncs(){return{getMonomer:(e,t)=>null,getMonomerSet:e=>({})}}_createDetachedHost(){let e=this._doc??rr();if(null===e)throw new Error("HelmHelperAdapter: no Document available");let t=e.createElement("div");return t.style.width="0px",t.style.height="0px",t.style.position="fixed",t}_ensureMolfilesEditor(){if(null!==this._molfilesEditor)return null!==this._molfilesGcTimer&&(clearTimeout(this._molfilesGcTimer),this._molfilesGcTimer=null),this._molfilesEditor;let e=this._createDetachedHost();return this._molfilesEditorHost=e,this._molfilesEditor=new Go(e,this._service,{width:100,height:100,...null!==this._doc?{documentImpl:this._doc}:{}}),this._logger,this._molfilesEditor}_scheduleMolfilesEditorGc(){null!==this._molfilesGcTimer&&clearTimeout(this._molfilesGcTimer),"function"==typeof setTimeout&&(this._molfilesGcTimer=setTimeout(()=>{this._molfilesGcTimer=null,this._removeMolfilesEditorNow()},e._MOLFILES_GC_MS))}_removeMolfilesEditorNow(){this._molfilesEditor=null,null!==this._molfilesEditorHost&&null!==this._molfilesEditorHost.parentNode&&this._molfilesEditorHost.parentNode.removeChild(this._molfilesEditorHost),this._molfilesEditorHost=null}};tr._MOLFILES_GC_MS=1e3;var ir,nr,or=tr;function rr(){return globalThis.document??null}function sr(e,t){if("string"==typeof e)return{biotype:e,symbol:t??null};if(null!==e&&"object"==typeof e&&"ATOM"===e.T){let i=e;return{biotype:i.bio.type,symbol:t??i.elem}}return{biotype:X,symbol:t??null}}function ar(e){switch(e){case X:return ne.PEPTIDE;case Q:case Z:case J:case ie:return ne.RNA;case ee:return ne.CHEM;case te:return ne.BLOB;default:return ne.PEPTIDE}}function lr(e,t){let i={};for(let t of e.rgroups)i[t.label]=t.capGroupName;let n={id:t??e.symbol,m:e.molfile,rs:e.rgroups.length,type:e.polymerType,mt:e.monomerType,at:i};return void 0!==e.name&&(n.n=e.name),void 0!==e.naturalAnalog&&(n.na=e.naturalAnalog),void 0!==e.smiles&&(n.smiles=e.smiles),n}function hr(e,t=!0){if(null==e)return"rgb(100,100,100)";const i=o.Color.fromHtml(e);if(t){const e=o.Color.g(i),t=o.Color.r(i),n=o.Color.b(i),r=Math.sqrt(Math.pow(0-t,2)+Math.pow(0-e,2)+Math.pow(0-n,2));if(r>210)return`rgb(${t/r*210},${e/r*210},${n/r*210})`}return o.Color.toRgb(i)}!function(e){e[e.default=0]="default",e[e.continuous=1]="continuous"}(ir||(ir={})),function(e){e.Sequence="sequence",e.Helm="notation",e.Properties="properties",e.StructureView="structureview"}(nr||(nr={}));class dr{static hashCode(e){let t=0;if(0===e.length)return t;for(let i=0;i<e.length;i++)t=(t<<5)-t+e.charCodeAt(i),t|=0;return t}}class cr{}class ur extends cr{static get palette(){return ur._pallete||(ur._pallete=ur.buildPalette()),ur._pallete}static buildPalette(){return v().then(e=>{e.awaitLoaded(1/0).then(()=>{const t=e.getMonomerLib();t.onChanged.subscribe(()=>{ur.customMonomerColors={},ur.polymerTypes=t.getPolymerTypes();for(const e of this.polymerTypes){const i=t.getMonomerSymbolsByType(e);for(const n of i){const i=t.getMonomer(e,n);i?.meta?.colors?.default?.background&&(this.customMonomerColors[n]||(this.customMonomerColors[n]={}),this.customMonomerColors[n][e]=hr(i.meta.colors.default.background))}}})})}),[].concat(...Object.values(g.colourPalette))}get(e,t){const i=ur.palette.length,n=ur.customMonomerColors[e],o=t??ne.PEPTIDE;if(n&&n[o])return n[o];const r=dr.hashCode(e)%i;return hr(ur.palette[r])}}ur._pallete=null,ur.customMonomerColors={},ur.polymerTypes=[];class pr extends o.JsInputBase{}async function mr(){const e="Helm",t=o.Func.find({package:e,name:"getHelmHelper"});if(0===t.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await t[0].prepare().call()).getOutputParamValue()}Error,t.input.helmAsync=async function(e,t){return(await mr()).createHelmInput(e,t)};const fr=/\{(\*\.)+/g,br=/\.(\*\.)+/g,gr=/(\.\*)+\}/g;class Ar extends Error{constructor(e,t){super(e,t)}}const _r=rxjs;class yr{onKeyDown(e,t){}onKeyPress(e,t){}onMouseEnter(e,t){}onMouseLeave(e,t){}onMouseDown(e,t){}onMouseUp(e,t){}onMouseMove(e,t){}onClick(e,t){}onDoubleClick(e,t){}}class vr extends yr{constructor(t,i,n){super(),this.gridCol=t,this.tableCol=i,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.cleanColVersion=-1,this.viewerId=++vr.viewerCounter,this.errors=[],this._onRendered=new _r.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.cleanColVersion=this.tableCol.version,this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe(()=>{this.tableCol?.version!==this.cleanColVersion&&(this.cleanColVersion=this.tableCol?.version,this.dirty=!0)})),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe(e=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(e){this.logger.error(e)}}))),this.tableCol&&this.subs.push(e.events.onTableRemoved.subscribe(e=>{try{const t=e.args.dataFrame;this.tableCol?.dataFrame.id!==t.id||this.destroyed||this.destroy()}catch(e){this.logger.error(e)}})),this.gridCol&&this.subs.push(e.events.onViewRemoving.subscribe(e=>{try{const t=e.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===t.id&&!this.destroyed&&this.destroy()}catch(e){this.logger.error(e)}}))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const e of this.subs)e.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(e){this.invalidateGrid()}async awaitRendered(e=1e4,t=`${e} timeout`){const i=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${i}, start, testEvent before`),await c(this._onRendered,()=>{},()=>{this.invalidate()},e,`${i}, ${t}`),this.errors.length>0){const e=this.errors[0];throw this.errors=[],e}this.logger.debug(`${i}, end`)}}var wr;vr.viewerCounter=-1,new RegExp("[rd]\\((\\w)\\)p?","g"),function(e){e[e.SUGAR=0]="SUGAR",e[e.BASE=1]="BASE",e[e.PHOSPHATE=2]="PHOSPHATE",e[e.TERMINAL_5P=3]="TERMINAL_5P",e[e.TERMINAL_3P=4]="TERMINAL_3P"}(wr||(wr={})),Map;function xr(e,t){try{const i=e.tableColumn;if(!i)return;const n=function(e){return e.temp.MonomerHoverLinks??[]}(i);for(let i=n.length-1;i>=0;--i){const o=n[i],r=e.grid.col(o.targetCol.name);if(r&&!o.handler(e,t,r))break}}catch(e){console.error(e)}}const Cr="bio.macromolecule.highlightMonomers",Er=o.Color.argb(255,255,220,0),kr=o.Color.argb(255,230,140,0);function Br(e,t){return`rgba(${o.Color.r(e)},${o.Color.g(e)},${o.Color.b(e)},${t??.4})`}function Sr(e,t,i,n){function o(n){let o,r;for(let s=0;s<i.atoms.length;++s)if(!n.includes(s)){const n=i.atoms[s].p.x,a=i.atoms[s].p.y,l=Math.sqrt((e-n)**2+(t-a)**2);(void 0===r||r>l)&&(o=s,r=l)}return[o,r]}const[r,s]=o([]),[a,l]=o([r]);let h=null;if(void 0!==r&&void 0!==s){const e=i.atoms[r];void 0!==a&&void 0!==l?s<.45*l&&(h=e):n&&s<.35*n&&(h=e)}return h}function Mr(e,t){const i=t.bio.continuousId-1;let n=t.elem;try{n=e.isDna()||e.isRna()?e.getSplittedWithSugarsAndPhosphates().getCanonical(i):e.getSplitted().getCanonical(i)}catch(e){}return{position:t.bio.continuousId-1,symbol:n,biotype:t.bio.type}}class Tr extends vr{cacheEnabled=!0;sysMonomerLib=null;helmHelper=null;serviceByLib=new Map;auxList=new Map;constructor(e,t){super(e,t,ds.logger)}async init(){await Promise.all([(async()=>{const e=await v();this.sysMonomerLib=e.getMonomerLib()})(),(async()=>{this.helmHelper=await mr()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe(()=>{for(const e of this.serviceByLib.values())e.destroy();this.serviceByLib.clear(),this.auxList.clear(),this.dirty=!0,this.invalidateGrid()})),this.subs.push(e.events.onCustomEvent("bio-macromolecule-monomer-highlight").subscribe(e=>this.handleHighlightEvent(e))),this.dirty=!0,this.invalidateGrid()}destroy(){for(const e of this.serviceByLib.values())e.destroy();this.serviceByLib.clear(),this.auxList.clear(),super.destroy()}handleHighlightEvent(e){if(!e||!this.tableCol||!this.tableCol.dataFrame)return;if(e.columnName!==this.tableCol.name)return;const t=this.tableCol.dataFrame;if(e.tableId&&t.id!==e.tableId)return;if(e.tableName&&t.name!==e.tableName)return;const i=this.tableCol.temp[Cr]??=new Map;null==e.monomers||0===e.monomers.length?i.delete(e.rowIdx):i.set(e.rowIdx,{monomers:e.monomers.slice(),fillColor:e.fillColor,strokeColor:e.strokeColor}),this.invalidateGrid()}getHighlightForRow(e){if(null==e)return null;const t=this.tableCol.temp[Cr];return t?.get(e)??null}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}getService(e){const t=e.source;let i=this.serviceByLib.get(t);return void 0===i&&(i=new sn({monomerLib:er(e)}),this.serviceByLib.set(t,i)),i}reset(){super.reset(),this.auxList=new Map,this.invalidateGrid()}render(e,t,i,n,r,s,a){const l=s.cell?.value;if(!l||null===this.sysMonomerLib)return;if(n<5||r<5)return;const h=window.devicePixelRatio,d=this.getService(this.getMonomerLib());e.save();try{e.resetTransform();const a=!(!this.gridCol?.dart||this.gridCol.grid?.canvas!==e.canvas),c={x:(a?s.bounds.x:t)*h,y:(a?s.bounds.y:i)*h,width:n*h,height:r*h},u=d.renderToCanvas(e,l,c,{maxScale:1/0,showIds:!1,showAnnotations:!0}),p={molView:zo(u.mol),bBox:new o.Rect(u.bbox.x,u.bbox.y,u.bbox.width,u.bbox.height),dBox:new o.Rect(u.drawBox.x,u.drawBox.y,u.drawBox.width,u.drawBox.height),cellHDev:r*h};this.auxList.set(l,p),this.drawHighlightOverlay(e,p,s.tableRowIndex)}catch(e){const[t,i]=m(e);this.logger.error(t,void 0,i)}finally{e.restore()}this._onRendered.next()}drawHighlightOverlay(e,t,i){const n=this.getHighlightForRow(i);if(!n||!n.monomers||0===n.monomers.length)return;const o=t.molView?.atoms;if(!o||0===o.length)return;if(t.bBox.width<=0||t.bBox.height<=0)return;const r=t.dBox.width/t.bBox.width,s=t.dBox.height/t.bBox.height,a=(r+s)/2,l=this.estimateMonomerRadiusModel(t),h=Math.max(6,l*a*.7),d=Math.max(1.5,.35*h),c=Br(n.fillColor??Er,.2),u=Br(n.strokeColor??kr);e.save();try{e.lineWidth=d,e.strokeStyle=u,e.fillStyle=c;for(const i of n.monomers){const n=o[i];if(!n||!n.p)continue;const a=t.dBox.x+(n.p.x-t.bBox.x)*r,l=t.dBox.y+(n.p.y-t.bBox.y)*s;e.beginPath(),e.arc(a,l,h,0,2*Math.PI),e.fill(),e.stroke()}}finally{e.restore()}}estimateMonomerRadiusModel(e){const t=e.molView?.bonds,i=[];if(t&&t.length>0)for(const e of t){const t=e?.a1?.p,n=e?.a2?.p;if(!t||!n)continue;const o=Math.hypot(t.x-n.x,t.y-n.y);o>0&&i.push(o)}if(i.length>0)return i.sort((e,t)=>e-t),.55*i[Math.floor(i.length/2)];const n=Math.max(1,e.molView?.atoms?.length??1);return.45*Math.sqrt(e.bBox.width*e.bBox.height/n)}onMouseMove(e,i){if(!e.cell?.value||i.buttons)return;const n=this.auxList.get(e.cell.value);if(!n)return;const o=`${this.toLog()}.onMouseMove()`,r=window.devicePixelRatio,s=e.bounds,a=(i.offsetX-s.x)*r,l=(i.offsetY-s.y)*r,h=n.dBox.x-s.x*r,d=n.dBox.y-s.y*r,c=n.bBox.x+(a-h)*n.bBox.width/n.dBox.width,u=n.bBox.y+(l-d)*n.bBox.height/n.dBox.height,p=n.cellHDev*n.bBox.height/n.dBox.height;if(!n.molView)return void this.logger.warning(`${o}, editorMol of the cell not found.`);const m=Sr(c,u,n.molView,p);let f=null;if(m&&this.helmHelper&&null!=e.tableRowIndex){f=Mr(this.helmHelper.seqHelper.getSeqHandler(this.tableCol).getValue(e.tableRowIndex),m);const n=this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??ds.monomerLib,o=n?n.getTooltip(f.biotype,f.symbol):t.divText("Monomer library is not available");t.tooltip.show(o,i.x+16,i.y+16)}else t.tooltip.hide();xr(e,f),i.preventDefault(),i.stopPropagation()}onMouseLeave(e,t){xr(e,null)}static getOrCreate(e){const[t,i,n]=function(e){let t=null,i=null;try{i=e.dart?e.gridColumn:null,t=i?i.temp:null}catch{[i,t]=[null,null]}const n=e.cell.column;if(t=t??(n?n.temp:null),!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[i,n,t]}(e);let o=n.rendererBack;return o||(o=n.rendererBack=new Tr(t,i),o.init().then(()=>{})),o}}class Ir extends o.GridCellRenderer{get name(){return"helm"}get cellType(){return"helm"}get defaultWidth(){return 400}get defaultHeight(){return 100}onMouseMove(e,t){try{Tr.getOrCreate(e).onMouseMove(e,t)}catch(e){const[t,i]=m(e);ds.logger.error(t,void 0,i)}}onMouseLeave(e,t){try{Tr.getOrCreate(e).onMouseLeave(e,t)}catch(e){const[t,i]=m(e);ds.logger.error(t,void 0,i)}finally{t.preventDefault(),t.stopPropagation()}}render(e,t,i,n,o,r,s){const a=36/window.devicePixelRatio;n<a||o<a||Tr.getOrCreate(r).render(e,t,i,n,o,r,s)}}function Lr(e){var t;return"string"==typeof e||e instanceof String?e:("object"==typeof e||e instanceof Object)&&"$thrownJsError"in e?Lr(e.$thrownJsError):e instanceof Error?null!==(t=e.stack)&&void 0!==t?t:e.message:e.toString()}class $r{constructor(e,t,i=""){this.target=e,this.debugEnabled=t,this.prefix=i}error(e,t,i){return this.target.error(this.prefix+e,t,i)}warning(e,t){return this.target.warning(this.prefix+e,t)}info(e,t){return this.target.info(this.prefix+e,t)}debug(e,t){if(this.debugEnabled)return this.target.debug(this.prefix+e,t)}}class Pr extends o.Package{_helmHelper;get helmHelper(){if(!this._helmHelper)throw new Error("Package Helm .helmHelper is not initialized");return this._helmHelper}get seqHelper(){return this.helmHelper.seqHelper}_libHelper;constructor(e={debug:!1}){super(),super._logger=new $r(super.logger,e.debug)}get monomerLib(){if(!this._libHelper)throw new Error("Helm: _package.libHelper is not initialized yet");return this._libHelper.getMonomerLib()}_monomerLibSub;_initialized=!1;completeInit(e,t){this._helmHelper=e,this._libHelper=t;const i=this.monomerLib;this._monomerLibSub=i.onChanged.subscribe(this.monomerLibOnChangedHandler.bind(this)),this._initialized=!0}monomerLibOnChangedHandler(){const t="Helm: _package.monomerLibOnChangedHandler()";try{const i=this.monomerLib.getSummaryObj(),n=0==Object.keys(i).length,o=n?"empty":Object.entries(i).map(([e,t])=>`${e}: ${t}`).join(", ");ds.logger.debug(`${t}, start, lib: { ${o} }`);const r=n?"empty":Object.entries(i).map(([e,t])=>`${e} ${t}`).join("<br />"),s=`Monomer lib updated:<br /> ${r}`;e.shell.info(s)}catch(e){const i=Lr(e);console.error(`${t} error:\n`+i)}}}class Rr extends pr{helmHelper;monomerLib;options;logger;get inputType(){return"Macromolecule"}get dataType(){return o.TYPE.STRING}getInput(){return this.viewerHost}_seqValue;getValue(){return this._seqValue}setValue(e){this._seqValue=e,this.viewer.editor.setHelm(this._seqValue.helm)}getStringValue(){return this._seqValue?.helm??""}setStringValue(e){if(!this._seqValue){let t;o.DataFrame.fromColumns([t=o.Column.fromList(o.COLUMN_TYPE.STRING,"seq",[e])]),t.semType=o.SEMTYPE.MACROMOLECULE,t.meta.units=l.HELM;const i=this.helmHelper.seqHelper.getSeqHandler(t);this._seqValue=i.getValue(0)}this.viewer.editor.setHelm(this._seqValue.value=e)}get molValue(){return this.viewer.editor.m}set molValue(e){this.viewer.editor.setMol(e),this._seqValue.value=this.viewer.editor.getHelm()}get onMouseMove(){return(0,_r.fromEvent)(this.viewer.host,"mousemove")}get onClick(){return(0,_r.fromEvent)(this.viewer.host,"click")}viewerHost;viewer;editHintDiv;helmString="";helmSelection;subs;constructor(e,i,n,o,r=ds.logger){super(),this.helmHelper=e,this.monomerLib=i,this.options=o,this.logger=r,n&&(this.captionLabel.innerText=n);const s=o?.editorOptions?.height??250,a=o?.editorOptions?.width??250;this.viewerHost=t.div([],{classes:"ui-input-editor",style:{width:`${a}px`,height:`${s}px`,minWidth:`${a}px`,minHeight:`${s}px`,overflow:"hidden"}}),this.viewer=this.helmHelper.createHelmWebEditor(this.viewerHost,{...o?.editorOptions,width:a,height:s}),this.editHintDiv=t.divH([t.link("Click to edit",()=>{this.viewer.host.click()},void 0,{})],{style:{display:"none",position:"absolute",top:"0",right:"0"}}),this.subs=[],this.subs.push(this.monomerLib.onChanged.subscribe(()=>this.viewer.editor.redraw())),(0,_r.fromEvent)(this.viewer.host,"mousemove").subscribe(this.viewerOnMouseMove.bind(this)),(0,_r.fromEvent)(this.viewer.host,"mouseenter").subscribe(this.viewerOnMouseEnter.bind(this)),(0,_r.fromEvent)(this.viewer.host,"mouseleave").subscribe(this.viewerOnMouseLeave.bind(this)),(0,_r.fromEvent)(this.viewer.host,"click").subscribe(this.viewerOnClick.bind(this)),this.subs.push(t.onSizeChanged(this.input).subscribe(()=>{const e=this.input.clientWidth,t=this.input.clientHeight;e>0&&t>0&&this.viewer.editor.setSize(e,t)})),this.root.classList.add("ui-input-helm"),this.root.append(this.viewerHost,this.editHintDiv)}detach(){for(const e of this.subs)e.unsubscribe()}toLog(){return"Helm: HelmInput<#>"}static create(e,t,i,n){const o=new Rr(e,t,i,n);return null!=n?.value&&(o.value=n.value),o}redraw(){this.viewer.editor.redraw()}showTooltip(e,i){const n=1.2*this.viewer.editor.getDrawOptions().fontsize,o=this.input.getBoundingClientRect();t.tooltip.show(e,o.left+i.p.x+n,o.top+i.p.y+n)}viewerOnClick(e){t.tooltip.hide(),0!=this.options?.editable&&this.showEditorDialog()}viewerOnMouseMove(e){this.toLog();const i=Sr(e.offsetX,e.offsetY,this.viewer.editor.m,this.viewer.editor.div.clientHeight);if(i){const n=Mr(this.value,i),o=ds.monomerLib,r=o?o.getTooltip(n.biotype,n.symbol):t.divText("Monomer library is not available");this.showTooltip(r,i),e.preventDefault(),e.stopPropagation()}else t.tooltip.hide()}viewerOnMouseEnter(e){0!=this.options?.editable&&this.showEditHint()}viewerOnMouseLeave(e){this.editHintDiv.contains(e.relatedTarget)||0!=this.options?.editable&&this.hideEditHint()}showEditHint(){this.editHintDiv.style.removeProperty("display")}hideEditHint(){this.editHintDiv.style.display="none"}showEditorDialog(){const i=t.div();i.style.height="100%";const n=this.helmHelper.createWebEditorApp(i,this.viewer.editor.getHelm()),o=()=>{s()(i).empty()};t.dialog({showHeader:!1,showFooter:!0}).add(i).onOK(()=>{try{const e=n.canvas.getHelm(!0).replace(/<\/span>/g,"").replace(/<span style='background:#bbf;'>/g,"");this.viewer.editor.setHelm(e),this.helmString=e;const t=n.canvas.helm.jsd.m.atoms;this.helmSelection=[];for(let e=0;e<t.length;e++)t[e].selected&&this.helmSelection.push(e),this.viewer.editor.m.atoms[e].highlighted=t[e].selected;this.viewer.editor.redraw()}catch(t){!function(t){const[i,n]=m(t);ds.logger.error(i,void 0,n),e.shell.error(i)}(t)}finally{o()}}).onCancel(()=>{o()}).show({modal:!0,fullScreen:!0})}}class Hr{seqHelper;logger;rdKitModule;static instanceCount=0;constructor(e,t,i){if(this.seqHelper=e,this.logger=t,this.rdKitModule=i,++Hr.instanceCount>1)throw new Error("HelmHelper must be a single.")}_editorAdapter=null;get editorAdapter(){if(null===this._editorAdapter){const e=ds._libHelper.getMonomerLib(),t=new Map;t.set("FASTA",async e=>this._toFastaProvider(e)),t.set("BILN",async e=>this._toBilnProvider(e)),t.set("Molecular Structure",async e=>this._atomicLevelProvider(e)),t.set("Composition Analysis",async e=>this._compositionAnalysisProvider(e));const i=new sn({monomerLib:er(e),rdkitModule:this.rdKitModule,extraPanes:t});this._editorAdapter=new or({service:i,seqHelper:this.seqHelper})}return this._editorAdapter}createHelmInput(e,t){try{const i=ds._libHelper.getMonomerLib();return Rr.create(this,i,e,t)}catch(e){const[t,i]=m(e);throw this.logger.error(`Helm: HelmHelper.createHelmInput(), Error: ${t}`,void 0,i),e}}createHelmWebEditor(e,t){return this.editorAdapter.createHelmWebEditor(e,{...void 0!==t?.width?{width:t.width}:{},...void 0!==t?.height?{height:t.height}:{}})}createWebEditorApp(e,t){return this.editorAdapter.createWebEditorApp(e,t)}get originalMonomersFuncs(){return this.editorAdapter.originalMonomersFuncs}revertOriginalMonomersFuncs(){return this.editorAdapter.revertOriginalMonomersFuncs()}overrideMonomersFuncs(e){return this.editorAdapter.overrideMonomersFuncs(e)}buildMonomersFuncsFromLib(e){return this.editorAdapter.buildMonomersFuncsFromLib(e)}getHoveredAtom(e,t,i,n){return Sr(e,t,i,n)}getMolfiles(e){return this.editorAdapter.getMolfiles(e)}parse(e,t){return this.editorAdapter.parse(e,t)}removeGaps(e){return this.editorAdapter.removeGaps(e)}_singeHelmDf=null;_getSingleHelmDf(e){if(null===this._singeHelmDf){const t=o.Column.fromStrings("helm",[e]);t.setTag("quality",o.SEMTYPE.MACROMOLECULE),t.setTag("units","helm"),t.setTag(".alphabetIsMultichar","true"),t.setTag("alphabet","UN");const i=Math.floor(.6*window.innerWidth);t.setTag(".toAtomicWidgetWidth",i.toString()),this._singeHelmDf=o.DataFrame.fromColumns([t])}return this._singeHelmDf.col("helm").set(0,e),this._singeHelmDf}_singleHelmSh=null;_getSingleHelmDfSh(e){if(!this._singleHelmSh){const t=this._getSingleHelmDf(e);this._singleHelmSh=this.seqHelper.getSeqHandler(t.col("helm"))}return this._singleHelmSh}async _atomicLevelProvider(t){const i=this._getSingleHelmDf(t),n=o.SemanticValue.fromTableCell(i.cell(0,"helm"));return(await e.functions.call("Bio:toAtomicLevelPanel",{sequence:n})).root}async _compositionAnalysisProvider(t){const i=this._getSingleHelmDf(t),n=o.SemanticValue.fromTableCell(i.cell(0,"helm"));return(await e.functions.call("Bio:compositionAnalysisWidget",{sequence:n})).root}_toBilnProvider(e){const i=this.editorAdapter.service.parse(e);if(i.mol.chains.length<1||i.mol.chains.some(e=>e.polymerType!==ne.PEPTIDE))return t.divText("Unsupported sequence for BILN");const n=this._getSingleHelmDfSh(e),o=t.input.textArea("",{});return o.value=n.getConverter(l.BILN)(e),o.input.setAttribute("disabled","true"),o.input.style.width="100%",o.input}_toFastaProvider(e){const i=this.editorAdapter.service.parse(e);if(1!==i.mol.chains.length||i.mol.atoms.length!==i.mol.bonds.filter(e=>"hbond"!==e.kind).length+1)return t.divText("Unsupported sequence for FASTA");const n=this._getSingleHelmDfSh(e),o=t.input.textArea("",{});return o.value=n.getConverter(l.FASTA)(e),o.input.setAttribute("disabled","true"),o.input.style.width="100%",o.input}}var Nr=i(72),Dr=i.n(Nr),Fr=i(825),Or=i.n(Fr),zr=i(659),Gr=i.n(zr),qr=i(56),jr=i.n(qr),Vr=i(540),Yr=i.n(Vr),Wr=i(113),Ur=i.n(Wr),Kr=i(130),Xr={};async function Qr(){await ps.initHelm()}function Zr(){return ps.helmCellRenderer()}function Jr(e){ps.editMoleculeCell(e)}function es(e){ps.openEditor(e)}async function ts(e){return await ps.propertiesWidget(e)}function is(e){return ps.getMolfiles(e)}function ns(e,t){return ps.helmInput(e,t)}function os(){return ps.getHelmHelper()}async function rs(){await ps.measureCellRenderer()}async function ss(){await ps.highlightMonomers()}Xr.styleTagTransform=Ur(),Xr.setAttributes=jr(),Xr.insert=Gr().bind(null,"head"),Xr.domAPI=Or(),Xr.insertStyleElement=Yr(),Dr()(Kr.A,Xr),Kr.A&&Kr.A.locals&&Kr.A.locals;var as=function(e,t,i,n){var o,r=arguments.length,s=r<3?t:null===n?n=Object.getOwnPropertyDescriptor(t,i):n;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)s=Reflect.decorate(e,t,i,n);else for(var a=e.length-1;a>=0;a--)(o=e[a])&&(s=(r<3?o(s):r>3?o(t,i,s):o(t,i))||s);return r>3&&s&&Object.defineProperty(t,i,s),s},ls=function(e,t){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(e,t)},hs=function(e,t){return function(i,n){t(i,n,e)}};const ds=new Pr;e.decorators||(e.decorators={}),["func","init","param","panel","editor","demo","app","appTreeBrowser","fileHandler","fileExporter","model","viewer","filter","cellRenderer","autostart","dashboard","folderViewer","semTypeDetector","packageSettingsEditor","functionAnalysis","converter","fileViewer","model","treeBrowser","polyfill"].forEach(t=>{e.decorators[t]||(e.decorators[t]=function(e){return function(e,t,i){}})});let cs=null;function us(e,i,n){!function(e,i,n){const o=t.div();o.style.height="100%";const r=e.cell.column,a=ds.seqHelper.getSeqHandler(r),l=ds.helmHelper.createWebEditorApp(o,e&&void 0===n?e.cell.value:i),h=t.dialog({showHeader:!1,showFooter:!0});h.add(o).onOK(()=>{const t=l.canvas.getHelm(!0).replace(/<\/span>/g,"").replace(/<span style='background:#bbf;'>/g,"");if(e)if(void 0===n)e.setValue(t);else{const i=a.convertHelmToFastaSeparator(t,n,a.separator);e.setValue(i)}}).show({modal:!0,fullScreen:!0});const d=s()(h.root).find("div").get()[0];d.className=d.className.replace("dlg- ui-form","dlg-ui-form")}(e,i,n)}class ps{static async initHelm(){return null===cs&&(cs=async function(){const t="Helm: _package.initHelm()";ds.logger.debug(`${t}, start`);try{const e=await async function(){const e=o.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()}(),t=await async function(){const e=o.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()}(),i=await v(),n=new Hr(t,ds.logger,e);ds.completeInit(n,i)}catch(i){const[n,o]=m(i);e.shell.error(`Package 'Helm' init error:\n${n}`);const r=new Error(`${t} error:\n ${n}\n${o}`);throw r.stack=o,r}finally{ds.logger.debug(`${t}, finally`)}ds.logger.debug(`${t}, end`)}()),cs}static helmCellRenderer(){return ds.logger.debug("Helm: _package.getHelmCellRenderer(), start"),new Ir}static editMoleculeCell(e){us(e,void 0,void 0)}static openEditor(t){const i=e.shell.tv.grid.dataFrame,n=i.columns.bySemType("Macromolecule"),r=ds.seqHelper.getSeqHandler(n),s=n.meta.units;if(-1===i.currentRowIdx)return;const a=o.GridCell.fromColumnRow(e.shell.tv.grid,n.name,i.currentRowIdx);s===l.HELM?us(a,void 0,void 0):us(a,r.getConverter(l.HELM)(t.value),n.meta.units)}static async propertiesWidget(e){return async function(e){const i=(await mr()).seqHelper.getSeqHandler(e.cell.column);try{const n=await async function(e,i){const n=t.div([],{style:{width:"0",height:"0"}});document.documentElement.appendChild(n);try{if(e.length>1e3)throw new Ar("Too long sequence to calculate molecular properties.");const t=(i.isHelm()?e:i.getConverter(l.HELM)(e)).replaceAll(fr,"{").replaceAll(br,".").replaceAll(gr,"}").replace("{*}","{}"),o=(await mr()).createHelmWebEditor(n).editor;o.setHelm(t);const r=o.getFormula(!0),s=Math.round(100*o.getMolWeight())/100,a=Math.round(100*o.getExtinctionCoefficient())/100;return{formula:r.replace(/<sub>/g,"").replace(/<\/sub>/g,""),"molecular weight":s,"extinction coefficient":a}}finally{s()(n).empty(),n.remove()}}(e.value,i);return new o.Widget(t.tableFromMap(n,!0))}catch(e){if(e instanceof Ar)return new o.Widget(t.divText(e.message));throw e}}(e)}static getMolfiles(e){const t=e.toList(),i=ds.helmHelper.getMolfiles(t);return o.Column.fromStrings("mols",i)}static helmInput(e,t){return ds.helmHelper.createHelmInput(e,t)}static getHelmHelper(){return ds.helmHelper}static async measureCellRenderer(){const t=e.shell.tv.grid,i=t.columns.byName("sequence").temp.rendererBack;let n=0,o=0;for(let e=0;e<20;++e){const e=window.performance.now();let r;i.cacheEnabled?await c(t.onAfterDrawContent,()=>{r=window.performance.now(),ds.logger.info(`measureCellRenderer() cache enabled, ET: ${r-e} ms`)},()=>{t.invalidate()},5e3):await c(i.onRendered,()=>{r=window.performance.now(),ds.logger.info(`measureCellRenderer() cache disabled , ET: ${r-e} ms`)},()=>{i.invalidate()},5e3),n+=r-e,o++}ds.logger.info(`measureCellRenderer(), avg ET: ${n/o} ms`)}static async highlightMonomers(){const t=o.TaskBarProgressIndicator.create("Test app highlight monomers");try{const t=await ds.files.readCsv("tests/peptide.csv");t.name="peptide.csv",await cs;const i=t.columns.byName("helm");await e.data.detectSemanticTypes(t),await e.functions.call("Bio:toAtomicLevel",{table:t,seqCol:i,nonlinear:!0,highlight:!0}),e.shell.addTableView(t)}finally{t.close()}}}as([e.decorators.init({tags:["init"]}),ls("design:type",Function),ls("design:paramtypes",[]),ls("design:returntype",Promise)],ps,"initHelm",null),as([e.decorators.func({meta:{columnTags:"quality=Macromolecule, units=helm",cellType:"helm",role:"cellRenderer"},tags:["cellRenderer"],outputs:[{name:"result",type:"grid_cell_renderer"}]}),ls("design:type",Function),ls("design:paramtypes",[]),ls("design:returntype",o.GridCellRenderer)],ps,"helmCellRenderer",null),as([e.decorators.func({meta:{columnTags:"quality=Macromolecule, units=helm",role:"cellEditor"},tags:["cellEditor"],description:"Macromolecule"}),hs(0,e.decorators.param({type:"grid_cell"})),ls("design:type",Function),ls("design:paramtypes",[o.GridCell]),ls("design:returntype",void 0)],ps,"editMoleculeCell",null),as([e.decorators.func({meta:{action:"Edit Helm..."},name:"Edit Helm...",description:"Adds editor"}),hs(0,e.decorators.param({options:{semType:"Macromolecule"}})),ls("design:type",Function),ls("design:paramtypes",[o.SemanticValue]),ls("design:returntype",void 0)],ps,"openEditor",null),as([e.decorators.panel({name:"Properties",meta:{role:"widgets",domain:"bio"},tags:["panel","widgets","bio"]}),hs(0,e.decorators.param({options:{semType:"Macromolecule"}})),ls("design:type",Function),ls("design:paramtypes",[o.SemanticValue]),ls("design:returntype",Promise)],ps,"propertiesWidget",null),as([e.decorators.func({name:"Get Molfiles from HELM",description:"Convert a column of HELM macromolecules into a column of molfiles"}),hs(0,e.decorators.param({type:"column",options:{semType:"Macromolecule"}})),ls("design:type",Function),ls("design:paramtypes",[o.Column]),ls("design:returntype",o.Column)],ps,"getMolfiles",null),as([e.decorators.func({meta:{propertyType:"string",semType:"Macromolecule",role:"valueEditor"},tags:["valueEditor"],outputs:[{type:"object",name:"result"}]}),hs(0,e.decorators.param({options:{optional:!0}})),hs(1,e.decorators.param({type:"object",options:{optional:!0}})),ls("design:type",Function),ls("design:paramtypes",[String,Object]),ls("design:returntype",pr)],ps,"helmInput",null),as([e.decorators.func({outputs:[{type:"object",name:"result"}]}),ls("design:type",Function),ls("design:paramtypes",[]),ls("design:returntype",Object)],ps,"getHelmHelper",null),as([e.decorators.func(),ls("design:type",Function),ls("design:paramtypes",[]),ls("design:returntype",Promise)],ps,"measureCellRenderer",null),as([e.decorators.func({name:"Highlight Monomers"}),ls("design:type",Function),ls("design:paramtypes",[]),ls("design:returntype",Promise)],ps,"highlightMonomers",null)})(),helm=n})();
1
+ var helm;(()=>{var e={717(e,t,i){"use strict";i.d(t,{j:()=>o});var n=i(82);async function o(){const e=n.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()}},599(e,t,i){"use strict";i.d(t,{kC:()=>r.kC});var n,o,r=i(199);!function(e){e[e.default=0]="default",e[e.continuous=1]="continuous"}(n||(n={})),function(e){e.Sequence="sequence",e.Helm="notation",e.Properties="properties",e.StructureView="structureview"}(o||(o={}))},124(e,t,i){"use strict";i.d(t,{KB:()=>r,b2:()=>s});var n=i(389),o=i(82);class r extends o.JsInputBase{}async function s(){const e="Helm",t=o.Func.find({package:e,name:"getHelmHelper"});if(0===t.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await t[0].prepare().call()).getOutputParamValue()}Error,n.input.helmAsync=async function(e,t){return(await s()).createHelmInput(e,t)}},971(e,t,i){"use strict";i.d(t,{pj:()=>o});var n=i(82);async function o(){const e=n.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===e.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await e[0].prepare().call()).getOutputParamValue()}},439(e,t,i){"use strict";i.d(t,{Hi:()=>n,_S:()=>l});var n,o,r,s=i(738);!function(e){e.FASTA="fasta",e.SEPARATOR="separator",e.HELM="helm",e.CUSTOM="custom",e.BILN="biln"}(n||(n={})),function(e){e.DNA="DNA",e.RNA="RNA",e.PT="PT",e.UN="UN"}(o||(o={})),function(e){e.aligned="aligned",e.alphabet="alphabet",e.alphabetSize=".alphabetSize",e.alphabetIsMultichar=".alphabetIsMultichar",e.separator="separator",e.isHelmCompatible=".isHelmCompatible",e.positionNames=".positionNames",e.positionLabels=".positionLabels",e.regions=".regions",e.positionShift=".positionShift",e.selectedPosition=".selectedPosition",e.polymerTypeColumnName=".polymerTypeColumnName",e.annotations=".annotations",e.numberingScheme=".numberingScheme",e.annotationColumnName=".annotationColumnName"}(r||(r={}));const a=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"])}}},l=(new s.aD(o.PT,a.fasta.peptide,.5),new s.aD(o.DNA,a.fasta.dna,.55),new s.aD(o.RNA,a.fasta.rna,.55),"");n.FASTA,n.SEPARATOR,n.HELM,n.BILN},3(e,t,i){"use strict";i.d(t,{Hi:()=>n.Hi});var n=i(439);i(291)},738(e,t,i){"use strict";i.d(t,{aD:()=>n}),i(439);class n{constructor(e,t,i){this.name=e,this.alphabet=t,this.cutoff=i}}},291(e,t,i){"use strict";var n=i(82);i(991),i(738),i(439);class o{static makePalette(e,t=!1,i=o){const n={};return e.forEach(e=>{const i=e[0],o=e[1];i.forEach((e,i)=>{n[e]=this.colourPalette[o][t?0:i]})}),new i(n)}constructor(e){this._palette=e}get(e,t){return this._palette[e]}}o.undefinedColor="rgb(100,100,100)",o.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class r extends o{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,r)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,r)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new r({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(e){const t=e in r.aaSynonyms?r.aaSynonyms[e]:e;return super.get(t)}}r.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class s{static getPalette(e="grok"){switch(e){case"grok":return r.GrokGroups;case"lesk":return r.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,i="",n="";for(const o of e)"("==o?t++:")"==o?t--:t?i+=o:n+=o;return isNaN(parseInt(i))?[n,i]:[n,""]}static getColorAAPivot(e="",t="grok"){const i=this.getPalette(t);let[n,o]=this.getInnerOuter(e);if(n=n.length>6?`${n.slice(0,3)}...`:n,o=o.length>6?`${o.slice(0,3)}...`:o,1==e.length||"("==e[1]){const t=e[0]?.toUpperCase();return t in i?[i.get(t),t,o,1]:[this.undefinedColor,n,o,1]}if("d"==e[0]&&e[1]in i&&(2==e.length||"("==e[2])){const t=e[1]?.toUpperCase();return t in i?[i.get(t),t,o,2]:[this.undefinedColor,n,o,2]}if(e.substring(0,3)in this.AAFullNames&&(3==e.length||"("==e[3])){const t=this.AAFullNames[e.substring(0,3)];return t in i?[i.get(t),t,o,3]:[this.undefinedColor,n,o,3]}if(e[0]?.toLowerCase()==e[0]&&e.substring(1,3)in this.AAFullNames&&(4==e.length||"("==e[4])){const t=this.AAFullNames[e.substring(1,3)];return t in i?[i.get(t),t,o,4]:[this.undefinedColor,n,o,4]}return[this.undefinedColor,n,o,0]}}s.SemType="Aminoacids",s.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",s.undefinedColor="rgb(100,100,100)",s.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},s.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},s.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},s.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class a{}a.SemType="Nucleotides",a.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",a.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};var l=i(971),h=i(599);function d(e,t=!0){if(null==e)return"rgb(100,100,100)";const i=n.Color.fromHtml(e);if(t){const e=n.Color.g(i),t=n.Color.r(i),o=n.Color.b(i),r=Math.sqrt(Math.pow(0-t,2)+Math.pow(0-e,2)+Math.pow(0-o,2));if(r>210)return`rgb(${t/r*210},${e/r*210},${o/r*210})`}return n.Color.toRgb(i)}class c{static hashCode(e){let t=0;if(0===e.length)return t;for(let i=0;i<e.length;i++)t=(t<<5)-t+e.charCodeAt(i),t|=0;return t}}class u{}class p extends u{static get palette(){return p._pallete||(p._pallete=p.buildPalette()),p._pallete}static buildPalette(){return(0,l.pj)().then(e=>{e.awaitLoaded(1/0).then(()=>{const t=e.getMonomerLib();t.onChanged.subscribe(()=>{p.customMonomerColors={},p.polymerTypes=t.getPolymerTypes();for(const e of this.polymerTypes){const i=t.getMonomerSymbolsByType(e);for(const n of i){const i=t.getMonomer(e,n);i?.meta?.colors?.default?.background&&(this.customMonomerColors[n]||(this.customMonomerColors[n]={}),this.customMonomerColors[n][e]=d(i.meta.colors.default.background))}}})})}),[].concat(...Object.values(o.colourPalette))}get(e,t){const i=p.palette.length,n=p.customMonomerColors[e],o=t??h.kC.PEPTIDE;if(n&&n[o])return n[o];const r=c.hashCode(e)%i;return d(p.palette[r])}}p._pallete=null,p.customMonomerColors={},p.polymerTypes=[]},312(e,t,i){"use strict";i.d(t,{Q:()=>o});var n=i(82);async function o(){const e=n.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()}},130(e,t,i){"use strict";i.d(t,{A:()=>a});var n=i(354),o=i.n(n),r=i(314),s=i.n(r)()(o());s.push([e.id,'/* T-0609 / Phase 19 (T-1902) / Phase 28 (T-2801, T-2804) --\n * Default editor stylesheet. SINGLE source of truth.\n *\n * Build pipeline:\n * 1. tsup copies this file byte-for-byte to `dist/editor.css`\n * (see `tsup.config.ts` -- onSuccess hook).\n * 2. `package.json#exports."./styles.css"` maps the public import\n * `@datagrok-libraries/hwe/styles.css` to `dist/editor.css`, so\n * library consumers do `import \'@datagrok-libraries/hwe/styles.css\';`\n * via their bundler (vite, webpack, rollup, etc.).\n * 3. apps/demo imports this file directly with a relative path\n * (`import \'../../../src/editor/styles/editor.css\';` in main.ts)\n * so vite serves source CSS in dev and bundles it in prod.\n *\n * Phase 28 removed the previous runtime injection path\n * (`injectAppStyles` + `editor-css.generated.ts` TS mirror). Reason:\n * dual delivery was a recurring drift hazard. The bundler is now the\n * SINGLE CSS-delivery channel; tests use `mountEditorCss` (in\n * `tests/helpers/load-css.ts`) to read this file directly when\n * stylesheet-text or `getComputedStyle` checks are needed in linkedom.\n */\n\n.hw-app {\n --hw-bg: #ffffff;\n --hw-fg: #1a1a1a;\n --hw-muted: #6c757d;\n --hw-accent: #1f5fcd;\n --hw-selection: #FFD29B;\n --hw-border: #d8d8d8;\n --hw-border-subtle: #e9ecef;\n --hw-tile-hover: #f1f3f5;\n --hw-toolbar-bg: #f4f5f7;\n --hw-pane-bg: #fafbfc;\n --hw-error: #cc0000;\n /* T-3517 -- toolbar icon stroke colour. Datagrok-style neutral grey\n (icons read as quiet chrome until hovered, then darken to --hw-fg). */\n --hw-icon: #6b7178;\n display: flex;\n flex-direction: column;\n width: 100%;\n height: 100%;\n background: var(--hw-bg);\n color: var(--hw-fg);\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 13px;\n box-sizing: border-box;\n}\n.hw-app--dark {\n --hw-bg: #1a1d23;\n --hw-fg: #e0e0e0;\n --hw-muted: #9aa1a8;\n --hw-accent: #6699ff;\n --hw-selection: #FFD29B;\n --hw-border: #3a3f47;\n --hw-border-subtle: #2c3037;\n --hw-tile-hover: #262a31;\n --hw-toolbar-bg: #22252b;\n --hw-pane-bg: #1f2228;\n --hw-error: #ff5050;\n --hw-icon: #9aa1a8;\n}\n.hw-app *, .hw-app *::before, .hw-app *::after { box-sizing: border-box; }\n\n.hw-app__toolbar { flex: 0 0 auto; }\n.hw-app__main {\n flex: 1 1 auto;\n display: flex;\n flex-direction: row;\n min-height: 0;\n border-top: 1px solid var(--hw-border);\n}\n.hw-app__palette {\n flex: 0 0 220px;\n border-right: 1px solid var(--hw-border);\n overflow: auto;\n background: var(--hw-pane-bg);\n}\n.hw-app__canvas { flex: 1 1 auto; position: relative; min-width: 0; overflow: hidden; }\n.hw-app__panes { flex: 0 0 auto; border-top: 1px solid var(--hw-border); }\n.hw-app__tabs { display: flex; flex-direction: row; background: var(--hw-toolbar-bg); }\n.hw-app__tab {\n padding: 6px 14px;\n cursor: pointer;\n border: none;\n background: transparent;\n color: var(--hw-fg);\n border-right: 1px solid var(--hw-border);\n font-size: 12px;\n}\n.hw-app__tab--active { background: var(--hw-bg); border-bottom: 2px solid var(--hw-accent); }\n/* Cap the active pane\'s height; taller content scrolls within the pane. */\n.hw-app__pane-body { padding: 8px; min-height: 80px; max-height: 300px; overflow: auto; background: var(--hw-bg); }\n\n.hw-toolbar {\n display: flex;\n flex-direction: row;\n align-items: center;\n gap: 4px;\n padding: 4px 6px;\n background: var(--hw-toolbar-bg);\n}\n.hw-toolbar__btn {\n /* T-3517 -- Datagrok-style flat, borderless icon buttons. The icon\n stroke uses the neutral grey --hw-icon; hover darkens it to --hw-fg\n and adds a soft rounded background, matching Datagrok\'s toolbar. */\n border: 1px solid transparent;\n background: transparent;\n color: var(--hw-icon);\n border-radius: 4px;\n padding: 5px;\n cursor: pointer;\n font-size: 13px;\n width: 30px;\n height: 30px;\n display: inline-flex;\n align-items: center;\n justify-content: center;\n transition: background 120ms, color 120ms;\n}\n.hw-toolbar__btn-icon {\n display: inline-block;\n width: 100%;\n height: 100%;\n color: inherit;\n}\n.hw-toolbar__btn-icon > svg {\n width: 100%;\n height: 100%;\n display: block;\n}\n.hw-toolbar__btn:hover { background: var(--hw-tile-hover, var(--hw-toolbar-bg)); color: var(--hw-fg); }\n.hw-toolbar__btn[disabled] { opacity: 0.4; cursor: default; }\n.hw-toolbar__btn--active {\n border-color: var(--hw-accent);\n background: var(--hw-accent);\n color: #ffffff;\n}\n.hw-toolbar__separator {\n display: inline-block;\n width: 1px;\n height: 18px;\n background: var(--hw-border);\n margin: 0 4px;\n}\n\n.hw-palette {\n display: flex;\n flex-direction: column;\n height: 100%;\n padding: 4px;\n}\n.hw-palette__search {\n width: 100%;\n padding: 4px;\n margin-bottom: 6px;\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n background: var(--hw-bg);\n color: var(--hw-fg);\n font-size: 12px;\n flex: 0 0 auto;\n}\n/* T-1421 / T-1423 -- tab list: horizontal row above the panes. Active\n tab gets a 2 px accent underline that absorbs the 1 px container\n border below via a negative bottom margin so the layout does not\n shift when the active tab changes.\n\n Phase 24 (T-2404): when a library exposes many polymer types\n (Favorites + PEPTIDE + RNA + CHEM + BLOB + G = 6 tabs), they can no\n longer fit horizontally inside the 200 px palette pane and the\n browser shows an unobvious horizontal scrollbar. Switch to\n `flex-wrap: wrap` so overflow tabs wrap onto a second (or third)\n row -- no hidden scrollbar, every tab is always visible. The\n per-tab padding shrinks too so more tabs fit per row before\n wrapping. */\n.hw-palette__tabs {\n display: flex;\n flex-wrap: wrap;\n gap: 2px 4px;\n border-bottom: 1px solid var(--hw-border);\n flex: 0 0 auto;\n /* Defensively: no overflow scrolling -- wrapping is the answer. */\n overflow: hidden;\n}\n.hw-palette__tab {\n /* Phase 24 (T-2404): compact padding + min-width so 6 tabs still fit\n in two rows max within a 200 px palette pane. */\n flex: 0 0 auto;\n padding: 6px 8px;\n cursor: pointer;\n border: none;\n background: transparent;\n font-size: 12px;\n color: var(--hw-muted);\n user-select: none;\n white-space: nowrap;\n min-width: 0;\n}\n.hw-palette__tab:hover {\n color: var(--hw-fg);\n background: var(--hw-tile-hover);\n}\n.hw-palette__tab[aria-selected="true"] {\n color: var(--hw-fg);\n border-bottom: 2px solid var(--hw-accent);\n margin-bottom: -1px;\n font-weight: 600;\n}\n.hw-palette__panes {\n flex: 1 1 auto;\n min-height: 0;\n}\n.hw-palette__pane {\n overflow-y: auto;\n max-height: 100%;\n padding: 4px 6px;\n}\n.hw-palette__pane[hidden] { display: none; }\n.hw-palette__placeholder {\n padding: 12px 6px;\n color: var(--hw-muted);\n font-size: 12px;\n font-style: italic;\n}\n/* T-1423 -- bolder, more separated group headers. */\n.hw-palette__group { margin-bottom: 12px; }\n.hw-palette__group-header {\n font-size: 13px;\n font-weight: 700;\n color: var(--hw-muted);\n padding: 8px 4px 4px;\n margin: 8px 0 4px;\n border-bottom: 1px solid var(--hw-border-subtle);\n text-transform: uppercase;\n letter-spacing: 0.04em;\n}\n.hw-palette__group-tiles {\n display: grid;\n grid-template-columns: repeat(3, 1fr);\n gap: 6px;\n padding: 2px;\n}\n.hw-palette__tiles { display: flex; flex-wrap: wrap; gap: 6px; padding: 2px; }\n.hw-palette__tile {\n position: relative;\n display: flex;\n flex-direction: column;\n align-items: center;\n justify-content: center;\n width: 100%;\n min-width: 48px;\n max-width: none;\n height: 40px;\n padding: 4px 6px;\n border: 2px solid var(--hw-border);\n border-radius: 8px;\n background: #ffffff;\n cursor: grab;\n font-size: 13px;\n font-weight: 600;\n user-select: none;\n overflow: hidden;\n text-overflow: ellipsis;\n box-shadow: 0 1px 2px rgba(0, 0, 0, 0.08);\n transition: border-color 120ms, transform 120ms, box-shadow 120ms;\n box-sizing: border-box;\n}\n.hw-palette__tile:hover {\n border-color: var(--hw-accent);\n transform: translateY(-1px);\n box-shadow: 0 2px 4px rgba(0, 0, 0, 0.12);\n}\n.hw-palette__tile[aria-pressed="true"],\n.hw-palette__tile--primed {\n border-color: var(--hw-accent);\n box-shadow: 0 0 0 2px rgba(31, 95, 205, 0.18);\n}\n.hw-palette__tile--favorite { outline: 1px dashed var(--hw-accent); outline-offset: -3px; }\n.hw-palette__tile--low-contrast {\n box-shadow: inset 0 0 0 1px rgba(0, 0, 0, 0.4), 0 1px 2px rgba(0, 0, 0, 0.08);\n}\n.hw-palette__star {\n position: absolute;\n top: 2px;\n right: 4px;\n font-size: 10px;\n cursor: pointer;\n color: var(--hw-muted);\n}\n.hw-palette__tile--favorite .hw-palette__star { color: var(--hw-accent); }\n.hw-palette__label {\n font-weight: 600;\n letter-spacing: 0.02em;\n display: inline-block;\n max-width: 80px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n}\n\n/* Phase 18 (T-1806) / Phase 19 (T-1903) / Phase 20 (T-2002) -- RNA Builder.\n Phase 20 redesign: SVG triplet visualization. Sugar (square),\n linker (circle), base (diamond) -- each clickable to enter pick\n mode. Fills come from the resolved monomer colour palette so the\n preview matches the canvas rendering. */\n.hw-rna-builder {\n display: block;\n /* Phase 21 (T-2101): horizontal margin nudges the builder rightward\n so it visually aligns with the palette tile column below. The\n user reported the SVG sat too far left vs. the tile rows. */\n margin: 4px 8px 12px;\n padding: 8px;\n background: var(--hw-pane-bg, #fafbfc);\n border: 1px solid var(--hw-border-subtle, #e9ecef);\n border-radius: 6px;\n}\n/* T-3513 -- header row holds the title plus the favorite star. */\n.hw-rna-builder__header {\n display: flex;\n align-items: center;\n justify-content: space-between;\n margin-bottom: 6px;\n}\n.hw-rna-builder__title {\n font-weight: 700;\n font-size: 12px;\n color: var(--hw-muted);\n text-transform: uppercase;\n letter-spacing: 0.04em;\n}\n.hw-rna-builder__header .hw-rna-builder__title {\n margin-bottom: 0;\n}\n/* T-3513 -- favorite star toggling the composed triplet. */\n.hw-rna-builder__fav {\n font-size: 15px;\n line-height: 1;\n cursor: pointer;\n color: var(--hw-muted);\n user-select: none;\n}\n.hw-rna-builder__fav--active { color: var(--hw-accent); }\n.hw-rna-builder__fav--disabled { opacity: 0.35; cursor: default; }\n/* Phase 29 (T-2901) -- Pick-mode hint shown directly under the "RNA\n builder" title while a slot is in pick mode. Replaces the Phase 24\n palette-level reserved-space hint above the search box. The hint\n carries the `hidden` HTML attribute when idle so the SVG triplet\n sits flush against the title (no wasted vertical space). User\n request 2026-05-19: "lets not have that empty space, and just\n display that text in bold below \'RNA BUILDER\' header, inside the\n builder itself." */\n.hw-rna-builder__hint {\n font-weight: 700;\n font-size: 12px;\n color: var(--hw-accent);\n margin: 4px 0 -14px;\n}\n.hw-rna-builder__hint[hidden] {\n display: none;\n}\n.hw-rna-builder__triplet {\n display: block;\n width: 100%;\n max-width: 180px;\n height: auto;\n max-height: 10vh;\n margin: 0 auto 6px;\n}\n.hw-rna-builder__bond {\n stroke: var(--hw-fg, #1a1a1a);\n stroke-width: 1.5;\n fill: none;\n}\n.hw-rna-builder__slot {\n cursor: pointer;\n}\n.hw-rna-builder__slot-shape {\n stroke-width: 1.5;\n transition: filter 120ms;\n}\n.hw-rna-builder__slot:hover .hw-rna-builder__slot-shape {\n filter: brightness(1.08);\n stroke-width: 2.5;\n}\n.hw-rna-builder__slot-label {\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n /* Phase 21 (T-2102): font-size is set per-label inline via\n setAttribute(\'font-size\', ...) so a long symbol like `[5meC]`\n can scale down. The CSS default below is a safety net for\n pre-T-2102 markup. */\n font-size: 12px;\n font-weight: 700;\n user-select: none;\n pointer-events: none;\n}\n.hw-rna-builder__slot--active .hw-rna-builder__slot-shape,\n.hw-rna-builder__slot[aria-pressed="true"] .hw-rna-builder__slot-shape {\n /* Yellow halo via filter so per-monomer fill / stroke stays intact. */\n filter: drop-shadow(0 0 3px #ffeb3b) drop-shadow(0 0 2px #ffeb3b);\n stroke-width: 2.5;\n}\n.hw-rna-builder__slot:focus {\n outline: none;\n}\n.hw-rna-builder__slot:focus-visible .hw-rna-builder__slot-shape {\n stroke: var(--hw-accent);\n stroke-width: 2.5;\n}\n.hw-rna-builder__preview {\n margin: 6px 0;\n font-size: 11px;\n color: var(--hw-fg);\n font-family: ui-monospace, Menlo, Consolas, monospace;\n text-align: center;\n}\n.hw-rna-builder__add {\n display: block;\n width: 100%;\n padding: 4px 8px;\n background: var(--hw-accent);\n color: #ffffff;\n border: 1px solid var(--hw-accent);\n border-radius: 3px;\n font-size: 12px;\n font-weight: 600;\n cursor: pointer;\n}\n.hw-rna-builder__add:hover { opacity: 0.9; }\n.hw-rna-builder__add:active { transform: translateY(1px); }\n\n/* T-3513 -- RNA triplet chips. Small, monospace, wrap into a tight row.\n Used by the RNA pane\'s default-nucleotide row (r(A)p ... r(T)p) and by\n triplet favorites in the Favorites pane. Kept compact because the RNA\n pane\'s vertical space is constrained by the RNA builder above it. */\n.hw-triplet-chips {\n display: flex;\n flex-wrap: wrap;\n gap: 4px;\n padding: 2px;\n}\n.hw-triplet-chips--defaults {\n margin: 0 0 8px;\n}\n.hw-triplet-chip {\n position: relative;\n display: inline-flex;\n align-items: center;\n gap: 2px;\n height: 22px;\n padding: 0 6px;\n border: 1px solid var(--hw-border);\n border-radius: 11px;\n font-family: ui-monospace, Menlo, Consolas, monospace;\n font-size: 11px;\n font-weight: 600;\n line-height: 1;\n cursor: pointer;\n user-select: none;\n box-shadow: 0 1px 1px rgba(0, 0, 0, 0.08);\n transition: border-color 120ms, transform 120ms;\n}\n.hw-triplet-chip:hover {\n border-color: var(--hw-accent);\n transform: translateY(-1px);\n}\n.hw-triplet-chip--favorite { border-color: var(--hw-accent); }\n.hw-triplet-chip__star {\n font-size: 10px;\n cursor: pointer;\n color: var(--hw-muted);\n}\n.hw-triplet-chip--favorite .hw-triplet-chip__star { color: var(--hw-accent); }\n.hw-triplet-chip__label { letter-spacing: 0.02em; }\n\n/* Phase 29 (T-2901) -- The Phase 24 palette-level pick-mode hint\n container has been REMOVED. The hint now lives inside the RNA\n Builder as `.hw-rna-builder__hint` (see the rules under the RNA\n Builder block above). The user explicitly reported the\n reserved-space hint above the search box as "wasted space". */\n\n.hw-pane { display: block; }\n.hw-pane__content { font-family: ui-monospace, Menlo, Consolas, monospace; font-size: 12px; white-space: pre-wrap; word-break: break-all; }\n.hw-pane__notation {\n outline: none;\n border: 1px solid var(--hw-border);\n padding: 4px;\n background: var(--hw-bg);\n}\n.hw-pane__error { color: var(--hw-error); font-size: 11px; margin-top: 4px; display: none; }\n.hw-pane__error--visible { display: block; }\n.hw-pane__prop-row { display: flex; gap: 8px; padding: 2px 0; }\n.hw-pane__prop-label { color: var(--hw-muted); width: 180px; }\n.hw-pane__prop-value { color: var(--hw-fg); }\n.hw-pane__placeholder { color: var(--hw-muted); font-style: italic; }\n\n.hw-pane__content.hw-pane__sequence, .hw-pane__content.hw-pane__notation {\n max-height: 100px;\n overflow: scroll;\n}\n\n.hw-modal-backdrop {\n position: absolute;\n top: 0; left: 0; right: 0; bottom: 0;\n background: rgba(0,0,0,0.3);\n display: flex; align-items: center; justify-content: center;\n z-index: 1000;\n}\n.hw-modal {\n background: var(--hw-bg);\n color: var(--hw-fg);\n border: 1px solid var(--hw-border);\n border-radius: 4px;\n min-width: 320px;\n max-width: 600px;\n padding: 12px;\n}\n.hw-modal__header { font-weight: bold; padding-bottom: 8px; border-bottom: 1px solid var(--hw-border); }\n.hw-modal__body { padding-top: 8px; }\n.hw-modal__row { display: flex; gap: 8px; align-items: center; padding: 4px 0; }\n.hw-modal__label { color: var(--hw-fg); min-width: 100px; }\n.hw-modal__input, .hw-modal__select {\n flex: 1;\n padding: 4px;\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n background: var(--hw-bg);\n color: var(--hw-fg);\n}\n.hw-modal__check { transform: scale(1.1); }\n.hw-modal__actions { display: flex; justify-content: flex-end; gap: 6px; padding-top: 10px; }\n.hw-modal__ok, .hw-modal__cancel, .hw-modal__find-next, .hw-modal__replace, .hw-modal__replace-all {\n padding: 4px 10px;\n border: 1px solid var(--hw-border);\n background: var(--hw-bg);\n color: var(--hw-fg);\n border-radius: 3px;\n cursor: pointer;\n}\n.hw-modal__ok { background: var(--hw-accent); color: #ffffff; border-color: var(--hw-accent); }\n.hw-modal__result { color: var(--hw-muted); font-size: 11px; padding-top: 6px; }\n\n/* Phase 23 (T-2304) -- Bond editor endpoint preview row. Renders two\n monomer structures (atom A1 and atom A2) flanking a `↔` arrow so the\n user can see what they\'re connecting while picking R-groups. The\n SVG inside each cell stretches via the .hw-bond-props__atom-rdkit\n svg rule below (matches the tooltip pattern). */\n.hw-bond-props__atoms {\n display: flex;\n align-items: center;\n gap: 16px;\n margin: 12px 0;\n}\n.hw-bond-props__atom {\n flex: 1;\n text-align: center;\n}\n.hw-bond-props__atom-label {\n font-weight: 600;\n margin-bottom: 6px;\n color: var(--hw-fg);\n}\n.hw-bond-props__atom-rdkit {\n width: 180px;\n height: 120px;\n margin: 0 auto 8px;\n background: #fafafa;\n border: 1px solid #f3f4f6;\n border-radius: 4px;\n padding: 4px;\n box-sizing: border-box;\n}\n.hw-bond-props__atom-rdkit svg {\n display: block;\n width: 100%;\n height: 100%;\n}\n.hw-bond-props__bond-arrow {\n font-size: 24px;\n color: var(--hw-muted);\n flex: 0 0 auto;\n}\n\n.hw-editor-view {\n width: 100%;\n height: 100%;\n position: relative;\n --hw-hover: #ff8c00;\n}\n.hw-editor-view svg { width: 100%; height: 100%; }\n\n/* T-1103 / Phase 19 (T-1901) -- Cursor affordance only. We removed\n the :hover rules that recoloured the atom\'s own outline because\n they ran in PARALLEL with the real highlight ring painted by the\n renderer (teal #26A69A), producing the wrong colour the user\n reported as "yellow on hover" (the CSS rule re-stroked the atom in\n var(--hw-hover) = #ff8c00, an orange-yellow). The renderer\'s\n highlight layer is now the single source of truth for hover\n feedback. */\n.hw-atom { cursor: pointer; }\n.hw-bond { cursor: pointer; }\n\n/* Mode-specific cursors on the canvas wrapper. The editor adds an\n hw-editor-view--<mode> class via the option:change handler. */\n.hw-editor-view--select svg { cursor: default; }\n.hw-editor-view--eraser svg { cursor: not-allowed; }\n.hw-editor-view--hbond svg { cursor: crosshair; }\n.hw-editor-view--move svg { cursor: grab; }\n.hw-editor-view--move:active svg { cursor: grabbing; }\n\n/* Phase 22 (T-2201) -- Unified tooltip styling. Three tooltip variants\n share the same look-and-feel: atom hover (canvas), bond hover\n (canvas), palette-tile hover (left pane), and rna-builder slot hover.\n Pre-Phase 22 the tooltips were absolutely-positioned, dark, and\n z-index 100 -- the gallery panel (z-index higher) ate into them and\n the dark background looked heavy. Phase 22 mounts the tooltip at\n `document.body` (escaping every parent stacking context), pins\n `z-index: 99999`, and paints them white with a soft drop shadow and\n darker body text so they read clearly over any backdrop. */\n/* Phase 32 (T-3003) -- Ghost cursor preview that follows the mouse\n when a palette tile is primed in select mode. `pointer-events:\n none` so the underlying canvas keeps receiving clicks / drags. The\n z-index sits just below the tooltips (99998 vs 99999) so a real\n tooltip can still overlay the ghost if both happen to be visible. */\n.hw-next-add-cursor {\n position: fixed;\n pointer-events: none;\n z-index: 99998;\n opacity: 0.7;\n display: none;\n}\n.hw-next-add-cursor__svg {\n display: block;\n}\n\n.hw-atom-tooltip,\n.hw-bond-tooltip,\n.hw-palette-tooltip,\n.hw-builder-tooltip,\n.hw-toolbar-tooltip {\n position: fixed;\n pointer-events: none;\n background: #ffffff;\n color: #1f2937;\n border: 1px solid #e5e7eb;\n border-radius: 6px;\n box-shadow: 0 4px 16px rgba(0, 0, 0, 0.12), 0 2px 4px rgba(0, 0, 0, 0.08);\n padding: 10px 12px;\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 12px;\n line-height: 1.4;\n max-width: 240px;\n z-index: 99999;\n}\n/* T-3516 -- toolbar button tooltip: a single compact line, no wrap. */\n.hw-toolbar-tooltip {\n padding: 5px 8px;\n white-space: nowrap;\n font-weight: 500;\n}\n.hw-tooltip__symbol {\n font-weight: 700;\n color: #111827;\n}\n/* T-3514 -- RNA triplet tooltip: three monomer structures side by side.\n Wider than the single-structure tooltip so all three columns fit. */\n.hw-triplet-tooltip { max-width: 420px; }\n.hw-tooltip__triplet {\n display: flex;\n gap: 8px;\n margin-top: 6px;\n}\n.hw-tooltip__triplet-part {\n flex: 1 1 0;\n min-width: 0;\n text-align: center;\n}\n.hw-tooltip__triplet-role {\n font-weight: 600;\n color: #111827;\n font-size: 11px;\n}\n.hw-tooltip__name {\n color: #4b5563;\n}\n.hw-tooltip__hint {\n color: #6b7280;\n font-style: italic;\n font-size: 11px;\n margin-top: 6px;\n}\n.hw-tooltip__rdkit {\n display: block;\n margin-top: 8px;\n /* padding-top: 8px; */\n border-top: 1px solid #f3f4f6;\n background: #fafafa;\n border-radius: 4px;\n}\n/* Phase 23 (T-2303) -- The user reported "molecules do not take the full\n space" in the tooltip. RDKit emits an svg with a `viewBox`, so\n `width: 100%; height: auto` lets the structure stretch responsively\n to whatever width the parent tooltip column has. `max-height` caps\n tall structures so they never blow up the tooltip vertically. */\n.hw-tooltip__rdkit svg,\n[data-testid="atom-tooltip-rdkit-svg"] svg,\n[data-testid="palette-tooltip-rdkit-svg"] svg,\n[data-testid="builder-tooltip-rdkit-svg"] svg {\n display: block;\n width: 100%;\n height: auto;\n max-height: 180px;\n margin: 0 auto;\n}\n/* Legacy aliases (kept so Phase 21 atom-tooltip text styling still\n resolves). The body text colour is now driven by the parent tooltip\n rule above; the legacy classes keep the line-wrap behaviour. */\n.hw-atom-tooltip__text {\n display: block;\n}\n\n/* Status indicator (T-1106) -- small badge in the bottom-left of the canvas. */\n.hw-status-bar {\n position: absolute;\n left: 6px;\n bottom: 6px;\n padding: 2px 8px;\n background: rgba(255, 255, 255, 0.85);\n color: var(--hw-fg);\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n font-size: 11px;\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n pointer-events: none;\n z-index: 50;\n}\n.hw-app--dark .hw-status-bar { background: rgba(34, 36, 41, 0.85); }\n\n.hw-status-bar__mode {\n display: inline-flex;\n align-items: center;\n gap: 0;\n}\n.hw-status-bar__message {\n display: inline-block;\n margin-left: 8px;\n font-weight: 500;\n}\n.hw-status-bar__message[data-severity="info"] { color: var(--hw-fg); }\n.hw-status-bar__message[data-severity="warn"] { color: #b8860b; }\n.hw-status-bar__message[data-severity="error"] { color: #c0392b; }\n.hw-app--dark .hw-status-bar__message[data-severity="warn"] { color: #f7c948; }\n.hw-app--dark .hw-status-bar__message[data-severity="error"] { color: #ff6b6b; }\n\n/* Phase 25 (T-2504) -- "Next add: X [x]" clear button. The status bar\n itself sets `pointer-events: none` (it floats above the canvas as a\n non-interactive badge), so the button explicitly re-enables hits on\n itself only. Visible only when `nextAdd` is primed because the\n element is conditionally appended in `_refreshStatus`. */\n.hw-status-bar__next-add-symbol {\n display: inline-block;\n font-weight: 600;\n}\n.hw-status-bar__next-add-clear {\n display: inline-flex;\n align-items: center;\n justify-content: center;\n width: 16px;\n height: 16px;\n margin-left: 6px;\n padding: 0;\n background: transparent;\n border: 1px solid #d1d5db;\n border-radius: 50%;\n color: #6b7280;\n font-size: 12px;\n line-height: 1;\n cursor: pointer;\n pointer-events: auto;\n}\n.hw-status-bar__next-add-clear:hover {\n background: #f3f4f6;\n color: #1f2937;\n border-color: #9ca3af;\n}\n\n.hw-bond-preview { pointer-events: none; opacity: 0.85; }\n\n.hw-help-modal-backdrop {\n position: fixed; left: 0; top: 0; right: 0; bottom: 0;\n background: rgba(0,0,0,0.4);\n display: flex; align-items: center; justify-content: center;\n z-index: 2000;\n}\n.hw-help-modal {\n background: #ffffff;\n color: #1a1a1a;\n padding: 16px 20px;\n border-radius: 4px;\n max-width: 480px;\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 13px;\n box-shadow: 0 10px 20px rgba(0,0,0,0.3);\n}\n.hw-help-modal h2 { margin: 0 0 8px 0; font-size: 16px; }\n.hw-help-modal ul { padding-left: 20px; line-height: 1.6; }\n.hw-help-modal kbd {\n background: #eef0f3;\n border: 1px solid #cbd0d6;\n border-radius: 3px;\n padding: 1px 4px;\n font-family: ui-monospace, Menlo, Consolas, monospace;\n font-size: 12px;\n}\n.hw-help-modal__close {\n margin-top: 12px;\n padding: 4px 12px;\n border: 1px solid #cbd0d6;\n background: #f5f6f8;\n cursor: pointer;\n border-radius: 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T-0609 / Phase 19 (T-1902) / Phase 28 (T-2801, T-2804) --\n * Default editor stylesheet. SINGLE source of truth.\n *\n * Build pipeline:\n * 1. tsup copies this file byte-for-byte to `dist/editor.css`\n * (see `tsup.config.ts` -- onSuccess hook).\n * 2. `package.json#exports."./styles.css"` maps the public import\n * `@datagrok-libraries/hwe/styles.css` to `dist/editor.css`, so\n * library consumers do `import \'@datagrok-libraries/hwe/styles.css\';`\n * via their bundler (vite, webpack, rollup, etc.).\n * 3. apps/demo imports this file directly with a relative path\n * (`import \'../../../src/editor/styles/editor.css\';` in main.ts)\n * so vite serves source CSS in dev and bundles it in prod.\n *\n * Phase 28 removed the previous runtime injection path\n * (`injectAppStyles` + `editor-css.generated.ts` TS mirror). Reason:\n * dual delivery was a recurring drift hazard. The bundler is now the\n * SINGLE CSS-delivery channel; tests use `mountEditorCss` (in\n * `tests/helpers/load-css.ts`) to read this file directly when\n * stylesheet-text or `getComputedStyle` checks are needed in linkedom.\n */\n\n.hw-app {\n --hw-bg: #ffffff;\n --hw-fg: #1a1a1a;\n --hw-muted: #6c757d;\n --hw-accent: #1f5fcd;\n --hw-selection: #FFD29B;\n --hw-border: #d8d8d8;\n --hw-border-subtle: #e9ecef;\n --hw-tile-hover: #f1f3f5;\n --hw-toolbar-bg: #f4f5f7;\n --hw-pane-bg: #fafbfc;\n --hw-error: #cc0000;\n /* T-3517 -- toolbar icon stroke colour. Datagrok-style neutral grey\n (icons read as quiet chrome until hovered, then darken to --hw-fg). */\n --hw-icon: #6b7178;\n display: flex;\n flex-direction: column;\n width: 100%;\n height: 100%;\n background: var(--hw-bg);\n color: var(--hw-fg);\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 13px;\n box-sizing: border-box;\n}\n.hw-app--dark {\n --hw-bg: #1a1d23;\n --hw-fg: #e0e0e0;\n --hw-muted: #9aa1a8;\n --hw-accent: #6699ff;\n --hw-selection: #FFD29B;\n --hw-border: #3a3f47;\n --hw-border-subtle: #2c3037;\n --hw-tile-hover: #262a31;\n --hw-toolbar-bg: #22252b;\n --hw-pane-bg: #1f2228;\n --hw-error: #ff5050;\n --hw-icon: #9aa1a8;\n}\n.hw-app *, .hw-app *::before, .hw-app *::after { box-sizing: border-box; }\n\n.hw-app__toolbar { flex: 0 0 auto; }\n.hw-app__main {\n flex: 1 1 auto;\n display: flex;\n flex-direction: row;\n min-height: 0;\n border-top: 1px solid var(--hw-border);\n}\n.hw-app__palette {\n flex: 0 0 220px;\n border-right: 1px solid var(--hw-border);\n overflow: auto;\n background: var(--hw-pane-bg);\n}\n.hw-app__canvas { flex: 1 1 auto; position: relative; min-width: 0; overflow: hidden; }\n.hw-app__panes { flex: 0 0 auto; border-top: 1px solid var(--hw-border); }\n.hw-app__tabs { display: flex; flex-direction: row; background: var(--hw-toolbar-bg); }\n.hw-app__tab {\n padding: 6px 14px;\n cursor: pointer;\n border: none;\n background: transparent;\n color: var(--hw-fg);\n border-right: 1px solid var(--hw-border);\n font-size: 12px;\n}\n.hw-app__tab--active { background: var(--hw-bg); border-bottom: 2px solid var(--hw-accent); }\n/* Cap the active pane\'s height; taller content scrolls within the pane. */\n.hw-app__pane-body { padding: 8px; min-height: 80px; max-height: 300px; overflow: auto; background: var(--hw-bg); }\n\n.hw-toolbar {\n display: flex;\n flex-direction: row;\n align-items: center;\n gap: 4px;\n padding: 4px 6px;\n background: var(--hw-toolbar-bg);\n}\n.hw-toolbar__btn {\n /* T-3517 -- Datagrok-style flat, borderless icon buttons. The icon\n stroke uses the neutral grey --hw-icon; hover darkens it to --hw-fg\n and adds a soft rounded background, matching Datagrok\'s toolbar. */\n border: 1px solid transparent;\n background: transparent;\n color: var(--hw-icon);\n border-radius: 4px;\n padding: 5px;\n cursor: pointer;\n font-size: 13px;\n width: 30px;\n height: 30px;\n display: inline-flex;\n align-items: center;\n justify-content: center;\n transition: background 120ms, color 120ms;\n}\n.hw-toolbar__btn-icon {\n display: inline-block;\n width: 100%;\n height: 100%;\n color: inherit;\n}\n.hw-toolbar__btn-icon > svg {\n width: 100%;\n height: 100%;\n display: block;\n}\n.hw-toolbar__btn:hover { background: var(--hw-tile-hover, var(--hw-toolbar-bg)); color: var(--hw-fg); }\n.hw-toolbar__btn[disabled] { opacity: 0.4; cursor: default; }\n.hw-toolbar__btn--active {\n border-color: var(--hw-accent);\n background: var(--hw-accent);\n color: #ffffff;\n}\n.hw-toolbar__separator {\n display: inline-block;\n width: 1px;\n height: 18px;\n background: var(--hw-border);\n margin: 0 4px;\n}\n\n.hw-palette {\n display: flex;\n flex-direction: column;\n height: 100%;\n padding: 4px;\n}\n.hw-palette__search {\n width: 100%;\n padding: 4px;\n margin-bottom: 6px;\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n background: var(--hw-bg);\n color: var(--hw-fg);\n font-size: 12px;\n flex: 0 0 auto;\n}\n/* T-1421 / T-1423 -- tab list: horizontal row above the panes. Active\n tab gets a 2 px accent underline that absorbs the 1 px container\n border below via a negative bottom margin so the layout does not\n shift when the active tab changes.\n\n Phase 24 (T-2404): when a library exposes many polymer types\n (Favorites + PEPTIDE + RNA + CHEM + BLOB + G = 6 tabs), they can no\n longer fit horizontally inside the 200 px palette pane and the\n browser shows an unobvious horizontal scrollbar. Switch to\n `flex-wrap: wrap` so overflow tabs wrap onto a second (or third)\n row -- no hidden scrollbar, every tab is always visible. The\n per-tab padding shrinks too so more tabs fit per row before\n wrapping. */\n.hw-palette__tabs {\n display: flex;\n flex-wrap: wrap;\n gap: 2px 4px;\n border-bottom: 1px solid var(--hw-border);\n flex: 0 0 auto;\n /* Defensively: no overflow scrolling -- wrapping is the answer. */\n overflow: hidden;\n}\n.hw-palette__tab {\n /* Phase 24 (T-2404): compact padding + min-width so 6 tabs still fit\n in two rows max within a 200 px palette pane. */\n flex: 0 0 auto;\n padding: 6px 8px;\n cursor: pointer;\n border: none;\n background: transparent;\n font-size: 12px;\n color: var(--hw-muted);\n user-select: none;\n white-space: nowrap;\n min-width: 0;\n}\n.hw-palette__tab:hover {\n color: var(--hw-fg);\n background: var(--hw-tile-hover);\n}\n.hw-palette__tab[aria-selected="true"] {\n color: var(--hw-fg);\n border-bottom: 2px solid var(--hw-accent);\n margin-bottom: -1px;\n font-weight: 600;\n}\n.hw-palette__panes {\n flex: 1 1 auto;\n min-height: 0;\n}\n.hw-palette__pane {\n overflow-y: auto;\n max-height: 100%;\n padding: 4px 6px;\n}\n.hw-palette__pane[hidden] { display: none; }\n.hw-palette__placeholder {\n padding: 12px 6px;\n color: var(--hw-muted);\n font-size: 12px;\n font-style: italic;\n}\n/* T-1423 -- bolder, more separated group headers. */\n.hw-palette__group { margin-bottom: 12px; }\n.hw-palette__group-header {\n font-size: 13px;\n font-weight: 700;\n color: var(--hw-muted);\n padding: 8px 4px 4px;\n margin: 8px 0 4px;\n border-bottom: 1px solid var(--hw-border-subtle);\n text-transform: uppercase;\n letter-spacing: 0.04em;\n}\n.hw-palette__group-tiles {\n display: grid;\n grid-template-columns: repeat(3, 1fr);\n gap: 6px;\n padding: 2px;\n}\n.hw-palette__tiles { display: flex; flex-wrap: wrap; gap: 6px; padding: 2px; }\n.hw-palette__tile {\n position: relative;\n display: flex;\n flex-direction: column;\n align-items: center;\n justify-content: center;\n width: 100%;\n min-width: 48px;\n max-width: none;\n height: 40px;\n padding: 4px 6px;\n border: 2px solid var(--hw-border);\n border-radius: 8px;\n background: #ffffff;\n cursor: grab;\n font-size: 13px;\n font-weight: 600;\n user-select: none;\n overflow: hidden;\n text-overflow: ellipsis;\n box-shadow: 0 1px 2px rgba(0, 0, 0, 0.08);\n transition: border-color 120ms, transform 120ms, box-shadow 120ms;\n box-sizing: border-box;\n}\n.hw-palette__tile:hover {\n border-color: var(--hw-accent);\n transform: translateY(-1px);\n box-shadow: 0 2px 4px rgba(0, 0, 0, 0.12);\n}\n.hw-palette__tile[aria-pressed="true"],\n.hw-palette__tile--primed {\n border-color: var(--hw-accent);\n box-shadow: 0 0 0 2px rgba(31, 95, 205, 0.18);\n}\n.hw-palette__tile--favorite { outline: 1px dashed var(--hw-accent); outline-offset: -3px; }\n.hw-palette__tile--low-contrast {\n box-shadow: inset 0 0 0 1px rgba(0, 0, 0, 0.4), 0 1px 2px rgba(0, 0, 0, 0.08);\n}\n.hw-palette__star {\n position: absolute;\n top: 2px;\n right: 4px;\n font-size: 10px;\n cursor: pointer;\n color: var(--hw-muted);\n}\n.hw-palette__tile--favorite .hw-palette__star { color: var(--hw-accent); }\n.hw-palette__label {\n font-weight: 600;\n letter-spacing: 0.02em;\n display: inline-block;\n max-width: 80px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n}\n\n/* Phase 18 (T-1806) / Phase 19 (T-1903) / Phase 20 (T-2002) -- RNA Builder.\n Phase 20 redesign: SVG triplet visualization. Sugar (square),\n linker (circle), base (diamond) -- each clickable to enter pick\n mode. Fills come from the resolved monomer colour palette so the\n preview matches the canvas rendering. */\n.hw-rna-builder {\n display: block;\n /* Phase 21 (T-2101): horizontal margin nudges the builder rightward\n so it visually aligns with the palette tile column below. The\n user reported the SVG sat too far left vs. the tile rows. */\n margin: 4px 8px 12px;\n padding: 8px;\n background: var(--hw-pane-bg, #fafbfc);\n border: 1px solid var(--hw-border-subtle, #e9ecef);\n border-radius: 6px;\n}\n/* T-3513 -- header row holds the title plus the favorite star. */\n.hw-rna-builder__header {\n display: flex;\n align-items: center;\n justify-content: space-between;\n margin-bottom: 6px;\n}\n.hw-rna-builder__title {\n font-weight: 700;\n font-size: 12px;\n color: var(--hw-muted);\n text-transform: uppercase;\n letter-spacing: 0.04em;\n}\n.hw-rna-builder__header .hw-rna-builder__title {\n margin-bottom: 0;\n}\n/* T-3513 -- favorite star toggling the composed triplet. */\n.hw-rna-builder__fav {\n font-size: 15px;\n line-height: 1;\n cursor: pointer;\n color: var(--hw-muted);\n user-select: none;\n}\n.hw-rna-builder__fav--active { color: var(--hw-accent); }\n.hw-rna-builder__fav--disabled { opacity: 0.35; cursor: default; }\n/* Phase 29 (T-2901) -- Pick-mode hint shown directly under the "RNA\n builder" title while a slot is in pick mode. Replaces the Phase 24\n palette-level reserved-space hint above the search box. The hint\n carries the `hidden` HTML attribute when idle so the SVG triplet\n sits flush against the title (no wasted vertical space). User\n request 2026-05-19: "lets not have that empty space, and just\n display that text in bold below \'RNA BUILDER\' header, inside the\n builder itself." */\n.hw-rna-builder__hint {\n font-weight: 700;\n font-size: 12px;\n color: var(--hw-accent);\n margin: 4px 0 -14px;\n}\n.hw-rna-builder__hint[hidden] {\n display: none;\n}\n.hw-rna-builder__triplet {\n display: block;\n width: 100%;\n max-width: 180px;\n height: auto;\n max-height: 10vh;\n margin: 0 auto 6px;\n}\n.hw-rna-builder__bond {\n stroke: var(--hw-fg, #1a1a1a);\n stroke-width: 1.5;\n fill: none;\n}\n.hw-rna-builder__slot {\n cursor: pointer;\n}\n.hw-rna-builder__slot-shape {\n stroke-width: 1.5;\n transition: filter 120ms;\n}\n.hw-rna-builder__slot:hover .hw-rna-builder__slot-shape {\n filter: brightness(1.08);\n stroke-width: 2.5;\n}\n.hw-rna-builder__slot-label {\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n /* Phase 21 (T-2102): font-size is set per-label inline via\n setAttribute(\'font-size\', ...) so a long symbol like `[5meC]`\n can scale down. The CSS default below is a safety net for\n pre-T-2102 markup. */\n font-size: 12px;\n font-weight: 700;\n user-select: none;\n pointer-events: none;\n}\n.hw-rna-builder__slot--active .hw-rna-builder__slot-shape,\n.hw-rna-builder__slot[aria-pressed="true"] .hw-rna-builder__slot-shape {\n /* Yellow halo via filter so per-monomer fill / stroke stays intact. */\n filter: drop-shadow(0 0 3px #ffeb3b) drop-shadow(0 0 2px #ffeb3b);\n stroke-width: 2.5;\n}\n.hw-rna-builder__slot:focus {\n outline: none;\n}\n.hw-rna-builder__slot:focus-visible .hw-rna-builder__slot-shape {\n stroke: var(--hw-accent);\n stroke-width: 2.5;\n}\n.hw-rna-builder__preview {\n margin: 6px 0;\n font-size: 11px;\n color: var(--hw-fg);\n font-family: ui-monospace, Menlo, Consolas, monospace;\n text-align: center;\n}\n.hw-rna-builder__add {\n display: block;\n width: 100%;\n padding: 4px 8px;\n background: var(--hw-accent);\n color: #ffffff;\n border: 1px solid var(--hw-accent);\n border-radius: 3px;\n font-size: 12px;\n font-weight: 600;\n cursor: pointer;\n}\n.hw-rna-builder__add:hover { opacity: 0.9; }\n.hw-rna-builder__add:active { transform: translateY(1px); }\n\n/* T-3513 -- RNA triplet chips. Small, monospace, wrap into a tight row.\n Used by the RNA pane\'s default-nucleotide row (r(A)p ... r(T)p) and by\n triplet favorites in the Favorites pane. Kept compact because the RNA\n pane\'s vertical space is constrained by the RNA builder above it. */\n.hw-triplet-chips {\n display: flex;\n flex-wrap: wrap;\n gap: 4px;\n padding: 2px;\n}\n.hw-triplet-chips--defaults {\n margin: 0 0 8px;\n}\n.hw-triplet-chip {\n position: relative;\n display: inline-flex;\n align-items: center;\n gap: 2px;\n height: 22px;\n padding: 0 6px;\n border: 1px solid var(--hw-border);\n border-radius: 11px;\n font-family: ui-monospace, Menlo, Consolas, monospace;\n font-size: 11px;\n font-weight: 600;\n line-height: 1;\n cursor: pointer;\n user-select: none;\n box-shadow: 0 1px 1px rgba(0, 0, 0, 0.08);\n transition: border-color 120ms, transform 120ms;\n}\n.hw-triplet-chip:hover {\n border-color: var(--hw-accent);\n transform: translateY(-1px);\n}\n.hw-triplet-chip--favorite { border-color: var(--hw-accent); }\n.hw-triplet-chip__star {\n font-size: 10px;\n cursor: pointer;\n color: var(--hw-muted);\n}\n.hw-triplet-chip--favorite .hw-triplet-chip__star { color: var(--hw-accent); }\n.hw-triplet-chip__label { letter-spacing: 0.02em; }\n\n/* Phase 29 (T-2901) -- The Phase 24 palette-level pick-mode hint\n container has been REMOVED. The hint now lives inside the RNA\n Builder as `.hw-rna-builder__hint` (see the rules under the RNA\n Builder block above). The user explicitly reported the\n reserved-space hint above the search box as "wasted space". */\n\n.hw-pane { display: block; }\n.hw-pane__content { font-family: ui-monospace, Menlo, Consolas, monospace; font-size: 12px; white-space: pre-wrap; word-break: break-all; }\n.hw-pane__notation {\n outline: none;\n border: 1px solid var(--hw-border);\n padding: 4px;\n background: var(--hw-bg);\n}\n.hw-pane__error { color: var(--hw-error); font-size: 11px; margin-top: 4px; display: none; }\n.hw-pane__error--visible { display: block; }\n.hw-pane__prop-row { display: flex; gap: 8px; padding: 2px 0; }\n.hw-pane__prop-label { color: var(--hw-muted); width: 180px; }\n.hw-pane__prop-value { color: var(--hw-fg); }\n.hw-pane__placeholder { color: var(--hw-muted); font-style: italic; }\n\n.hw-pane__content.hw-pane__sequence, .hw-pane__content.hw-pane__notation {\n max-height: 100px;\n overflow: scroll;\n}\n\n.hw-modal-backdrop {\n position: absolute;\n top: 0; left: 0; right: 0; bottom: 0;\n background: rgba(0,0,0,0.3);\n display: flex; align-items: center; justify-content: center;\n z-index: 1000;\n}\n.hw-modal {\n background: var(--hw-bg);\n color: var(--hw-fg);\n border: 1px solid var(--hw-border);\n border-radius: 4px;\n min-width: 320px;\n max-width: 600px;\n padding: 12px;\n}\n.hw-modal__header { font-weight: bold; padding-bottom: 8px; border-bottom: 1px solid var(--hw-border); }\n.hw-modal__body { padding-top: 8px; }\n.hw-modal__row { display: flex; gap: 8px; align-items: center; padding: 4px 0; }\n.hw-modal__label { color: var(--hw-fg); min-width: 100px; }\n.hw-modal__input, .hw-modal__select {\n flex: 1;\n padding: 4px;\n border: 1px solid var(--hw-border);\n border-radius: 3px;\n background: var(--hw-bg);\n color: var(--hw-fg);\n}\n.hw-modal__check { transform: scale(1.1); }\n.hw-modal__actions { display: flex; justify-content: flex-end; gap: 6px; padding-top: 10px; }\n.hw-modal__ok, .hw-modal__cancel, .hw-modal__find-next, .hw-modal__replace, .hw-modal__replace-all {\n padding: 4px 10px;\n border: 1px solid var(--hw-border);\n background: var(--hw-bg);\n color: var(--hw-fg);\n border-radius: 3px;\n cursor: pointer;\n}\n.hw-modal__ok { background: var(--hw-accent); color: #ffffff; border-color: var(--hw-accent); }\n.hw-modal__result { color: var(--hw-muted); font-size: 11px; padding-top: 6px; }\n\n/* Phase 23 (T-2304) -- Bond editor endpoint preview row. Renders two\n monomer structures (atom A1 and atom A2) flanking a `↔` arrow so the\n user can see what they\'re connecting while picking R-groups. The\n SVG inside each cell stretches via the .hw-bond-props__atom-rdkit\n svg rule below (matches the tooltip pattern). */\n.hw-bond-props__atoms {\n display: flex;\n align-items: center;\n gap: 16px;\n margin: 12px 0;\n}\n.hw-bond-props__atom {\n flex: 1;\n text-align: center;\n}\n.hw-bond-props__atom-label {\n font-weight: 600;\n margin-bottom: 6px;\n color: var(--hw-fg);\n}\n.hw-bond-props__atom-rdkit {\n width: 180px;\n height: 120px;\n margin: 0 auto 8px;\n background: #fafafa;\n border: 1px solid #f3f4f6;\n border-radius: 4px;\n padding: 4px;\n box-sizing: border-box;\n}\n.hw-bond-props__atom-rdkit svg {\n display: block;\n width: 100%;\n height: 100%;\n}\n.hw-bond-props__bond-arrow {\n font-size: 24px;\n color: var(--hw-muted);\n flex: 0 0 auto;\n}\n\n.hw-editor-view {\n width: 100%;\n height: 100%;\n position: relative;\n --hw-hover: #ff8c00;\n}\n.hw-editor-view svg { width: 100%; height: 100%; }\n\n/* T-1103 / Phase 19 (T-1901) -- Cursor affordance only. We removed\n the :hover rules that recoloured the atom\'s own outline because\n they ran in PARALLEL with the real highlight ring painted by the\n renderer (teal #26A69A), producing the wrong colour the user\n reported as "yellow on hover" (the CSS rule re-stroked the atom in\n var(--hw-hover) = #ff8c00, an orange-yellow). The renderer\'s\n highlight layer is now the single source of truth for hover\n feedback. */\n.hw-atom { cursor: pointer; }\n.hw-bond { cursor: pointer; }\n\n/* Mode-specific cursors on the canvas wrapper. The editor adds an\n hw-editor-view--<mode> class via the option:change handler. */\n.hw-editor-view--select svg { cursor: default; }\n.hw-editor-view--eraser svg { cursor: not-allowed; }\n.hw-editor-view--hbond svg { cursor: crosshair; }\n.hw-editor-view--move svg { cursor: grab; }\n.hw-editor-view--move:active svg { cursor: grabbing; }\n\n/* Phase 22 (T-2201) -- Unified tooltip styling. Three tooltip variants\n share the same look-and-feel: atom hover (canvas), bond hover\n (canvas), palette-tile hover (left pane), and rna-builder slot hover.\n Pre-Phase 22 the tooltips were absolutely-positioned, dark, and\n z-index 100 -- the gallery panel (z-index higher) ate into them and\n the dark background looked heavy. Phase 22 mounts the tooltip at\n `document.body` (escaping every parent stacking context), pins\n `z-index: 99999`, and paints them white with a soft drop shadow and\n darker body text so they read clearly over any backdrop. */\n/* Phase 32 (T-3003) -- Ghost cursor preview that follows the mouse\n when a palette tile is primed in select mode. `pointer-events:\n none` so the underlying canvas keeps receiving clicks / drags. The\n z-index sits just below the tooltips (99998 vs 99999) so a real\n tooltip can still overlay the ghost if both happen to be visible. */\n.hw-next-add-cursor {\n position: fixed;\n pointer-events: none;\n z-index: 99998;\n opacity: 0.7;\n display: none;\n}\n.hw-next-add-cursor__svg {\n display: block;\n}\n\n.hw-atom-tooltip,\n.hw-bond-tooltip,\n.hw-palette-tooltip,\n.hw-builder-tooltip,\n.hw-toolbar-tooltip {\n position: fixed;\n pointer-events: none;\n background: #ffffff;\n color: #1f2937;\n border: 1px solid #e5e7eb;\n border-radius: 6px;\n box-shadow: 0 4px 16px rgba(0, 0, 0, 0.12), 0 2px 4px rgba(0, 0, 0, 0.08);\n padding: 10px 12px;\n font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n font-size: 12px;\n line-height: 1.4;\n max-width: 240px;\n z-index: 99999;\n}\n/* T-3516 -- toolbar button tooltip: a single compact line, no wrap. */\n.hw-toolbar-tooltip {\n padding: 5px 8px;\n white-space: nowrap;\n font-weight: 500;\n}\n.hw-tooltip__symbol {\n font-weight: 700;\n color: #111827;\n}\n/* T-3514 -- RNA triplet tooltip: three monomer structures side by side.\n Wider than the single-structure tooltip so all three columns fit. */\n.hw-triplet-tooltip { max-width: 420px; }\n.hw-tooltip__triplet {\n display: flex;\n gap: 8px;\n margin-top: 6px;\n}\n.hw-tooltip__triplet-part {\n flex: 1 1 0;\n min-width: 0;\n text-align: center;\n}\n.hw-tooltip__triplet-role {\n font-weight: 600;\n color: #111827;\n font-size: 11px;\n}\n.hw-tooltip__name {\n color: #4b5563;\n}\n.hw-tooltip__hint {\n color: #6b7280;\n font-style: italic;\n font-size: 11px;\n margin-top: 6px;\n}\n.hw-tooltip__rdkit {\n display: block;\n margin-top: 8px;\n /* padding-top: 8px; */\n border-top: 1px solid #f3f4f6;\n background: #fafafa;\n border-radius: 4px;\n}\n/* Phase 23 (T-2303) -- The user reported "molecules do not take the full\n space" in the tooltip. RDKit emits an svg with a `viewBox`, so\n `width: 100%; height: auto` lets the structure stretch responsively\n to whatever width the parent tooltip column has. `max-height` caps\n tall structures so they never blow up the tooltip vertically. */\n.hw-tooltip__rdkit svg,\n[data-testid="atom-tooltip-rdkit-svg"] svg,\n[data-testid="palette-tooltip-rdkit-svg"] svg,\n[data-testid="builder-tooltip-rdkit-svg"] svg {\n display: block;\n width: 100%;\n height: auto;\n max-height: 180px;\n margin: 0 auto;\n}\n/* Legacy aliases (kept so Phase 21 atom-tooltip text styling still\n resolves). 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Map;null==e.monomers||0===e.monomers.length?i.delete(e.rowIdx):i.set(e.rowIdx,{monomers:e.monomers.slice(),fillColor:e.fillColor,strokeColor:e.strokeColor}),this.invalidateGrid()}getHighlightForRow(e){if(null==e)return null;const t=this.tableCol.temp[k];return t?.get(e)??null}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}getService(e){const t=e.source;let i=this.serviceByLib.get(t);return void 0===i&&(i=new M.Cs({monomerLib:(0,M.a)(e)}),this.serviceByLib.set(t,i)),i}reset(){super.reset(),this.auxList=new Map,this.invalidateGrid()}render(e,t,i,n,o,s,a){const l=s.cell?.value;if(!l||null===this.sysMonomerLib)return;if(n<5||o<5)return;const h=window.devicePixelRatio,d=this.getService(this.getMonomerLib());e.save();try{e.resetTransform();const 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r=t.dBox.width/t.bBox.width,s=t.dBox.height/t.bBox.height,a=(r+s)/2,l=this.estimateMonomerRadiusModel(t),h=Math.max(6,l*a*.7),d=Math.max(1.5,.35*h),c=S(n.fillColor??E,.2),u=S(n.strokeColor??B);e.save();try{e.lineWidth=d,e.strokeStyle=u,e.fillStyle=c;for(const i of n.monomers){const n=o[i];if(!n||!n.p)continue;const a=t.dBox.x+(n.p.x-t.bBox.x)*r,l=t.dBox.y+(n.p.y-t.bBox.y)*s;e.beginPath(),e.arc(a,l,h,0,2*Math.PI),e.fill(),e.stroke()}}finally{e.restore()}}estimateMonomerRadiusModel(e){const t=e.molView?.bonds,i=[];if(t&&t.length>0)for(const e of t){const t=e?.a1?.p,n=e?.a2?.p;if(!t||!n)continue;const o=Math.hypot(t.x-n.x,t.y-n.y);o>0&&i.push(o)}if(i.length>0)return i.sort((e,t)=>e-t),.55*i[Math.floor(i.length/2)];const n=Math.max(1,e.molView?.atoms?.length??1);return.45*Math.sqrt(e.bBox.width*e.bBox.height/n)}onMouseMove(e,t){if(!e.cell?.value||t.buttons)return;const i=this.auxList.get(e.cell.value);if(!i)return;const n=`${this.toLog()}.onMouseMove()`,r=window.devicePixelRatio,s=e.bounds,a=(t.offsetX-s.x)*r,l=(t.offsetY-s.y)*r,h=i.dBox.x-s.x*r,d=i.dBox.y-s.y*r,c=i.bBox.x+(a-h)*i.bBox.width/i.dBox.width,u=i.bBox.y+(l-d)*i.bBox.height/i.dBox.height,p=i.cellHDev*i.bBox.height/i.dBox.height;if(!i.molView)return void this.logger.warning(`${n}, editorMol of the cell not found.`);const m=T(c,u,i.molView,p);let f=null;if(m&&this.helmHelper&&null!=e.tableRowIndex){f=I(this.helmHelper.seqHelper.getSeqHandler(this.tableCol).getValue(e.tableRowIndex),m);const i=this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??fe.monomerLib,n=i?i.getTooltip(f.biotype,f.symbol):o.divText("Monomer library is not available");o.tooltip.show(n,t.x+16,t.y+16)}else o.tooltip.hide();C(e,f),t.preventDefault(),t.stopPropagation()}onMouseLeave(e,t){C(e,null)}static getOrCreate(e){const[t,i,n]=function(e){let t=null,i=null;try{i=e.dart?e.gridColumn:null,t=i?i.temp:null}catch{[i,t]=[null,null]}const n=e.cell.column;if(t=t??(n?n.temp:null),!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[i,n,t]}(e);let o=n.rendererBack;return o||(o=n.rendererBack=new L(t,i),o.init().then(()=>{})),o}}class $ extends r.GridCellRenderer{get name(){return"helm"}get cellType(){return"helm"}get defaultWidth(){return 400}get defaultHeight(){return 100}onMouseMove(e,t){try{L.getOrCreate(e).onMouseMove(e,t)}catch(e){const[t,i]=u(e);fe.logger.error(t,void 0,i)}}onMouseLeave(e,t){try{L.getOrCreate(e).onMouseLeave(e,t)}catch(e){const[t,i]=u(e);fe.logger.error(t,void 0,i)}finally{t.preventDefault(),t.stopPropagation()}}render(e,t,i,n,o,r,s){const a=36/window.devicePixelRatio;n<a||o<a||L.getOrCreate(r).render(e,t,i,n,o,r,s)}}function P(e){var t;return"string"==typeof e||e instanceof String?e:("object"==typeof e||e instanceof Object)&&"$thrownJsError"in e?P(e.$thrownJsError):e instanceof Error?null!==(t=e.stack)&&void 0!==t?t:e.message:e.toString()}class R{constructor(e,t,i=""){this.target=e,this.debugEnabled=t,this.prefix=i}error(e,t,i){return this.target.error(this.prefix+e,t,i)}warning(e,t){return this.target.warning(this.prefix+e,t)}info(e,t){return this.target.info(this.prefix+e,t)}debug(e,t){if(this.debugEnabled)return this.target.debug(this.prefix+e,t)}}var H=i(413);class N extends r.Package{_helmHelper;get helmHelper(){if(!this._helmHelper)throw new Error("Package Helm .helmHelper is not initialized");return this._helmHelper}get seqHelper(){return this.helmHelper.seqHelper}_libHelper;constructor(e={debug:!1}){super(),super._logger=new R(super.logger,e.debug)}get monomerLib(){if(!this._libHelper)throw new Error("Helm: _package.libHelper is not initialized yet");return this._libHelper.getMonomerLib()}_monomerLibSub;_initialized=!1;get defaultMonomersPerRow(){let e;try{e=this.settings?.MonomersPerRow}catch{e=void 0}return(0,H.U)(e)}applyDefaultMonomersPerRow(){(0,M.Y$)(this.defaultMonomersPerRow)}completeInit(e,t){this._helmHelper=e,this._libHelper=t;const i=this.monomerLib;this._monomerLibSub=i.onChanged.subscribe(this.monomerLibOnChangedHandler.bind(this)),this._initialized=!0}monomerLibOnChangedHandler(){const e="Helm: _package.monomerLibOnChangedHandler()";try{const t=this.monomerLib.getSummaryObj(),i=0==Object.keys(t).length,o=i?"empty":Object.entries(t).map(([e,t])=>`${e}: ${t}`).join(", ");fe.logger.debug(`${e}, start, lib: { ${o} }`);const r=`Monomer lib updated:<br /> ${i?"empty":Object.entries(t).map(([e,t])=>`${e} ${t}`).join("<br />")}`;n.shell.info(r)}catch(t){const i=P(t);console.error(`${e} error:\n`+i)}}}class D extends f.KB{helmHelper;monomerLib;options;logger;get inputType(){return"Macromolecule"}get dataType(){return r.TYPE.STRING}getInput(){return this.viewerHost}_seqValue;getValue(){return this._seqValue}setValue(e){this._seqValue=e,this.viewer.editor.setHelm(this._seqValue.helm)}getStringValue(){return this._seqValue?.helm??""}setStringValue(e){if(!this._seqValue){let t;r.DataFrame.fromColumns([t=r.Column.fromList(r.COLUMN_TYPE.STRING,"seq",[e])]),t.semType=r.SEMTYPE.MACROMOLECULE,t.meta.units=p.Hi.HELM;const i=this.helmHelper.seqHelper.getSeqHandler(t);this._seqValue=i.getValue(0)}this.viewer.editor.setHelm(this._seqValue.value=e)}get molValue(){return this.viewer.editor.m}set molValue(e){this.viewer.editor.setMol(e),this._seqValue.value=this.viewer.editor.getHelm()}get onMouseMove(){return(0,_.fromEvent)(this.viewer.host,"mousemove")}get onClick(){return(0,_.fromEvent)(this.viewer.host,"click")}viewerHost;viewer;editHintDiv;helmString="";helmSelection;subs;constructor(e,t,i,n,r=fe.logger){super(),this.helmHelper=e,this.monomerLib=t,this.options=n,this.logger=r,i&&(this.captionLabel.innerText=i);const s=n?.editorOptions?.height??250,a=n?.editorOptions?.width??250;this.viewerHost=o.div([],{classes:"ui-input-editor",style:{width:`${a}px`,height:`${s}px`,minWidth:`${a}px`,minHeight:`${s}px`,overflow:"hidden"}}),this.viewer=this.helmHelper.createHelmWebEditor(this.viewerHost,{...n?.editorOptions,width:a,height:s}),this.editHintDiv=o.divH([o.link("Click to edit",()=>{this.viewer.host.click()},void 0,{})],{style:{display:"none",position:"absolute",top:"0",right:"0"}}),this.subs=[],this.subs.push(this.monomerLib.onChanged.subscribe(()=>this.viewer.editor.redraw())),(0,_.fromEvent)(this.viewer.host,"mousemove").subscribe(this.viewerOnMouseMove.bind(this)),(0,_.fromEvent)(this.viewer.host,"mouseenter").subscribe(this.viewerOnMouseEnter.bind(this)),(0,_.fromEvent)(this.viewer.host,"mouseleave").subscribe(this.viewerOnMouseLeave.bind(this)),(0,_.fromEvent)(this.viewer.host,"click").subscribe(this.viewerOnClick.bind(this)),this.subs.push(o.onSizeChanged(this.input).subscribe(()=>{const e=this.input.clientWidth,t=this.input.clientHeight;e>0&&t>0&&this.viewer.editor.setSize(e,t)})),this.root.classList.add("ui-input-helm"),this.root.append(this.viewerHost,this.editHintDiv)}detach(){for(const e of this.subs)e.unsubscribe()}toLog(){return"Helm: HelmInput<#>"}static create(e,t,i,n){const o=new D(e,t,i,n);return null!=n?.value&&(o.value=n.value),o}redraw(){this.viewer.editor.redraw()}showTooltip(e,t){const i=1.2*this.viewer.editor.getDrawOptions().fontsize,n=this.input.getBoundingClientRect();o.tooltip.show(e,n.left+t.p.x+i,n.top+t.p.y+i)}viewerOnClick(e){o.tooltip.hide(),0!=this.options?.editable&&this.showEditorDialog()}viewerOnMouseMove(e){this.toLog();const t=T(e.offsetX,e.offsetY,this.viewer.editor.m,this.viewer.editor.div.clientHeight);if(t){const i=I(this.value,t),n=fe.monomerLib,r=n?n.getTooltip(i.biotype,i.symbol):o.divText("Monomer library is not available");this.showTooltip(r,t),e.preventDefault(),e.stopPropagation()}else o.tooltip.hide()}viewerOnMouseEnter(e){0!=this.options?.editable&&this.showEditHint()}viewerOnMouseLeave(e){this.editHintDiv.contains(e.relatedTarget)||0!=this.options?.editable&&this.hideEditHint()}showEditHint(){this.editHintDiv.style.removeProperty("display")}hideEditHint(){this.editHintDiv.style.display="none"}showEditorDialog(){const e=o.div();e.style.height="100%";const t=this.helmHelper.createWebEditorApp(e,this.viewer.editor.getHelm()),i=()=>{a()(e).empty()};o.dialog({showHeader:!1,showFooter:!0}).add(e).onOK(()=>{try{const e=t.canvas.getHelm(!0).replace(/<\/span>/g,"").replace(/<span style='background:#bbf;'>/g,"");this.setStringValue(e),this.helmString=e;const i=t.canvas.helm.jsd.m.atoms;this.helmSelection=[];for(let e=0;e<i.length;e++)i[e].selected&&this.helmSelection.push(e),this.viewer.editor.m.atoms[e].highlighted=i[e].selected;this.viewer.editor.redraw(),this.fireChanged()}catch(e){!function(e){const[t,i]=u(e);fe.logger.error(t,void 0,i),n.shell.error(t)}(e)}finally{i()}}).onCancel(()=>{i()}).show({modal:!0,fullScreen:!0})}}class F{seqHelper;logger;rdKitModule;static instanceCount=0;constructor(e,t,i){if(this.seqHelper=e,this.logger=t,this.rdKitModule=i,++F.instanceCount>1)throw new Error("HelmHelper must be a single.")}_editorAdapter=null;get editorAdapter(){if(null===this._editorAdapter){const e=fe._libHelper.getMonomerLib(),t=new Map;t.set("FASTA",async e=>this._toFastaProvider(e)),t.set("BILN",async e=>this._toBilnProvider(e)),t.set("Molecular Structure",async e=>this._atomicLevelProvider(e)),t.set("Composition Analysis",async e=>this._compositionAnalysisProvider(e));const i=new M.Cs({monomerLib:(0,M.a)(e),rdkitModule:this.rdKitModule,extraPanes:t});this._editorAdapter=new M.eo({service:i,seqHelper:this.seqHelper})}return this._editorAdapter}createHelmInput(e,t){try{const i=fe._libHelper.getMonomerLib();return D.create(this,i,e,t)}catch(e){const[t,i]=u(e);throw this.logger.error(`Helm: HelmHelper.createHelmInput(), Error: ${t}`,void 0,i),e}}createHelmWebEditor(e,t){return this.editorAdapter.createHelmWebEditor(e,{...void 0!==t?.width?{width:t.width}:{},...void 0!==t?.height?{height:t.height}:{}})}createWebEditorApp(e,t){return this.editorAdapter.createWebEditorApp(e,t)}get originalMonomersFuncs(){return this.editorAdapter.originalMonomersFuncs}revertOriginalMonomersFuncs(){return this.editorAdapter.revertOriginalMonomersFuncs()}overrideMonomersFuncs(e){return this.editorAdapter.overrideMonomersFuncs(e)}buildMonomersFuncsFromLib(e){return this.editorAdapter.buildMonomersFuncsFromLib(e)}getHoveredAtom(e,t,i,n){return T(e,t,i,n)}getMolfiles(e){return this.editorAdapter.getMolfiles(e)}parse(e,t){return this.editorAdapter.parse(e,t)}removeGaps(e){return this.editorAdapter.removeGaps(e)}_singeHelmDf=null;_getSingleHelmDf(e){if(null===this._singeHelmDf){const t=r.Column.fromStrings("helm",[e]);t.setTag("quality",r.SEMTYPE.MACROMOLECULE),t.setTag("units","helm"),t.setTag(".alphabetIsMultichar","true"),t.setTag("alphabet","UN");const i=Math.floor(.6*window.innerWidth);t.setTag(".toAtomicWidgetWidth",i.toString()),this._singeHelmDf=r.DataFrame.fromColumns([t])}return this._singeHelmDf.col("helm").set(0,e),this._singeHelmDf}_singleHelmSh=null;_getSingleHelmDfSh(e){if(!this._singleHelmSh){const t=this._getSingleHelmDf(e);this._singleHelmSh=this.seqHelper.getSeqHandler(t.col("helm"))}return this._singleHelmSh}async _atomicLevelProvider(e){const t=this._getSingleHelmDf(e),i=r.SemanticValue.fromTableCell(t.cell(0,"helm"));return(await n.functions.call("Bio:toAtomicLevelPanel",{sequence:i})).root}async _compositionAnalysisProvider(e){const t=this._getSingleHelmDf(e),i=r.SemanticValue.fromTableCell(t.cell(0,"helm"));return(await n.functions.call("Bio:compositionAnalysisWidget",{sequence:i})).root}_toBilnProvider(e){const t=this.editorAdapter.service.parse(e);if(t.mol.chains.length<1||t.mol.chains.some(e=>e.polymerType!==M.kC.PEPTIDE))return o.divText("Unsupported sequence for BILN");const i=this._getSingleHelmDfSh(e),n=o.input.textArea("",{});return n.value=i.getConverter(p.Hi.BILN)(e),n.input.setAttribute("disabled","true"),n.input.style.width="100%",n.input}_toFastaProvider(e){const t=this.editorAdapter.service.parse(e);if(1!==t.mol.chains.length||t.mol.atoms.length!==t.mol.bonds.filter(e=>"hbond"!==e.kind).length+1)return o.divText("Unsupported sequence for FASTA");const i=this._getSingleHelmDfSh(e),n=o.input.textArea("",{});return n.value=i.getConverter(p.Hi.FASTA)(e),n.input.setAttribute("disabled","true"),n.input.style.width="100%",n.input}}var O=i(717),z=i(72),G=i.n(z),q=i(825),j=i.n(q),Y=i(659),V=i.n(Y),W=i(56),U=i.n(W),K=i(540),X=i.n(K),Q=i(113),Z=i.n(Q),J=i(130),ee={};async function te(){await Ae.initHelm()}function ie(){return Ae.helmCellRenderer()}function ne(e){Ae.editMoleculeCell(e)}async function oe(e){return await Ae.helmPanel(e)}function re(e){Ae.openEditor(e)}async function se(e){return await Ae.propertiesWidget(e)}function ae(e){return Ae.getMolfiles(e)}function le(e,t){return Ae.helmInput(e,t)}function he(){return Ae.getHelmHelper()}async function de(){await Ae.measureCellRenderer()}async function ce(){await Ae.highlightMonomers()}ee.styleTagTransform=Z(),ee.setAttributes=U(),ee.insert=V().bind(null,"head"),ee.domAPI=j(),ee.insertStyleElement=X(),G()(J.A,ee),J.A&&J.A.locals&&J.A.locals;var ue=function(e,t,i,n){var o,r=arguments.length,s=r<3?t:null===n?n=Object.getOwnPropertyDescriptor(t,i):n;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)s=Reflect.decorate(e,t,i,n);else for(var a=e.length-1;a>=0;a--)(o=e[a])&&(s=(r<3?o(s):r>3?o(t,i,s):o(t,i))||s);return r>3&&s&&Object.defineProperty(t,i,s),s},pe=function(e,t){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(e,t)},me=function(e,t){return function(i,n){t(i,n,e)}};const fe=new N;n.decorators||(n.decorators={}),["func","init","param","panel","editor","demo","app","appTreeBrowser","fileHandler","fileExporter","model","viewer","filter","cellRenderer","autostart","dashboard","folderViewer","semTypeDetector","packageSettingsEditor","functionAnalysis","converter","fileViewer","model","treeBrowser","polyfill"].forEach(e=>{n.decorators[e]||(n.decorators[e]=function(e){return function(e,t,i){}})});let be=null;function ge(e,t,i){!function(e,t,i){const n=o.div();n.style.height="100%";const r=e.cell.column,s=fe.seqHelper.getSeqHandler(r),l=fe.helmHelper.createWebEditorApp(n,e&&void 0===i?e.cell.value:t),h=o.dialog({showHeader:!1,showFooter:!0});h.add(n).onOK(()=>{const t=l.canvas.getHelm(!0).replace(/<\/span>/g,"").replace(/<span style='background:#bbf;'>/g,"");if(e)if(void 0===i)e.setValue(t);else{const n=s.convertHelmToFastaSeparator(t,i,s.separator);e.setValue(n)}}).show({modal:!0,fullScreen:!0});const d=a()(h.root).find("div").get()[0];d.className=d.className.replace("dlg- ui-form","dlg-ui-form")}(e,t,i)}class Ae{static async initHelm(){return null===be&&(be=async function(){const e="Helm: _package.initHelm()";fe.logger.debug(`${e}, start`);try{const e=await(0,O.j)(),t=await(0,m.Q)(),i=await(0,b.pj)(),n=new F(t,fe.logger,e);fe.completeInit(n,i),fe.applyDefaultMonomersPerRow()}catch(t){const[i,o]=u(t);n.shell.error(`Package 'Helm' init error:\n${i}`);const r=new Error(`${e} error:\n ${i}\n${o}`);throw r.stack=o,r}finally{fe.logger.debug(`${e}, finally`)}fe.logger.debug(`${e}, end`)}()),be}static helmCellRenderer(){return fe.logger.debug("Helm: _package.getHelmCellRenderer(), start"),new $}static editMoleculeCell(e){ge(e,void 0,void 0)}static async helmPanel(e){return e.meta.units!==p.Hi.HELM?new r.Widget(o.divText("These settings apply only to HELM columns")):(0,A.P)()}static openEditor(e){const t=n.shell.tv.grid.dataFrame,i=t.columns.bySemType("Macromolecule"),o=fe.seqHelper.getSeqHandler(i),s=i.meta.units;if(-1===t.currentRowIdx)return;const a=r.GridCell.fromColumnRow(n.shell.tv.grid,i.name,t.currentRowIdx);s===p.Hi.HELM?ge(a,void 0,void 0):ge(a,o.getConverter(p.Hi.HELM)(e.value),i.meta.units)}static async propertiesWidget(e){return(0,g.AY)(e)}static getMolfiles(e){const t=e.toList(),i=fe.helmHelper.getMolfiles(t);return r.Column.fromStrings("mols",i)}static helmInput(e,t){return fe.helmHelper.createHelmInput(e,t)}static getHelmHelper(){return fe.helmHelper}static async measureCellRenderer(){const e=n.shell.tv.grid,t=e.columns.byName("sequence").temp.rendererBack;let i=0,o=0;for(let n=0;n<20;++n){const n=window.performance.now();let r;t.cacheEnabled?await h(e.onAfterDrawContent,()=>{r=window.performance.now(),fe.logger.info(`measureCellRenderer() cache enabled, ET: ${r-n} ms`)},()=>{e.invalidate()},5e3):await 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if(!0===this.options.legacyCaseFallback&&"RNA"===t){let o=this.findCaseInsensitiveMatch(t,e.symbol);null!==o&&(i=this.toResolved(o),n=ne(o)??e.biotype,this.emit("info","case-mismatch",`Symbol '${e.symbol}' matched library entry '${o.symbol}' only after case fold`,e))}null===i&&(i=this.synthesizeMissing(t,e),this.emit("warning","unresolved-monomer",`Monomer '${e.symbol}' not found in library for ${t}`,e))}return{...e,monomer:i,biotype:n}}toResolved(e){let t=this.lib.getResolved?.(e);if(void 0!==t)return t;let i=new Map;for(let t of e.rgroups){let e=se.exec(t.label);null!==e&&i.set(parseInt(e[1],10),t)}return Object.assign({},e,{rs:e.rgroups.length,rgroupMap:i})}isAmbiguitySymbol(e){return!(!re.has(e.symbol)&&void 0===e.bio.ambiguity)}synthesizeAmbiguity(e,t){let i=`ambig:${e}:${t.symbol}`,n=this.placeholderCache.get(i);return void 0===n&&(n={symbol:t.symbol,polymerType:e,monomerType:"Undefined",molfile:"",rgroups:[{label:"R1",capGroupName:"H",capGroupSMILES:""},{label:"R2",capGroupName:"H",capGroupSMILES:""}],meta:{ambiguous:!0}},this.placeholderCache.set(i,n)),this.toResolved(n)}synthesizeMissing(e,t){let i=`missing:${e}:${t.symbol}`,n=this.placeholderCache.get(i);return void 0===n&&(n={symbol:t.symbol,polymerType:e,monomerType:"Undefined",molfile:"",rgroups:[{label:"R1",capGroupName:"H",capGroupSMILES:""},{label:"R2",capGroupName:"H",capGroupSMILES:""}],meta:{missing:!0}},this.placeholderCache.set(i,n)),this.toResolved(n)}registerInlineSmilesFallback(e,t){if("function"==typeof this.lib.registerInlineSmilesMonomer)try{let i=this.lib.registerInlineSmilesMonomer(e,t.symbol);return this.toResolved(i)}catch{this.emit("warning","inline-smiles-without-r-groups",`Inline SMILES '${i=t.symbol,i.length<=40?i:i.slice(0,39)+"…"}' has no detectable R-groups`,t)}else this.emit("warning","inline-smiles-without-r-groups","Inline SMILES seen but lib has no registerInlineSmilesMonomer",t);var i;return this.synthesizeMissing(e,t)}findCaseInsensitiveMatch(e,t){let i=t.toLowerCase();for(let n of this.lib.getMonomerSymbolsByType(e))if(n.toLowerCase()===i&&n!==t){let t=this.lib.getMonomer(e,n);if(null!==t)return t}return null}emit(e,t,i,n){let o={chainId:n.bio.chainId,atomId:n.id,symbol:n.symbol};this.diagnostics.push({severity:e,code:t,message:i,context:o})}};function le(e,t,i){let n,o=i?.mode??"lenient";try{n=function(e){let t=new p(e).tokenize();return function(e){let t=null;for(let i of e.tokens)if("apos"===i.kind)t=null===t?i.span:null;else if("eof"===i.kind&&null!==t)throw new r("unterminated-apostrophe",`Unterminated apostrophe block starting at offset ${t.start}`,{span:{start:t.start,end:e.source.length}})}(t),t}(e)}catch(e){if(e instanceof r){if("strict"===o)throw e;let t={severity:"error",code:e.code,message:e.message,...void 0!==e.span?{span:{start:e.span.start,end:e.span.end}}:{}};return{mol:b(),diagnostics:[t]}}throw e}return function(e,t,i){let n=new ue(e,t,i?.mode??"lenient").parseDocument();if(null===t||!1===i?.resolveMonomers)return n;let o=oe(n.mol,t,{mode:i?.mode??"lenient",...!0===i?.legacyCaseFallback?{legacyCaseFallback:!0}:{}});return{mol:o.mol,diagnostics:[...n.diagnostics,...o.diagnostics]}}(n,t,i)}var he=class{constructor(e){this.tokens=e.tokens,this.len=e.tokens.length,this.eof=e.tokens[e.tokens.length-1],this.idx=0}peek(e=0){let t=this.idx+e;return t>=this.len?this.eof:this.tokens[t]}advance(){let e=this.idx<this.len?this.tokens[this.idx]:this.eof;return"eof"!==e.kind&&(this.idx+=1),e}optional(e){let t=this.idx<this.len?this.tokens[this.idx]:this.eof;return t.kind===e?("eof"!==t.kind&&(this.idx+=1),t):null}at(e){return(this.idx<this.len?this.tokens[this.idx]:this.eof).kind===e}at2(e,t){let i=(this.idx<this.len?this.tokens[this.idx]:this.eof).kind;return i===e||i===t}at3(e,t,i){let n=(this.idx<this.len?this.tokens[this.idx]:this.eof).kind;return n===e||n===t||n===i}currentSpan(){return(this.idx<this.len?this.tokens[this.idx]:this.eof).span}position(){return this.idx}setPosition(e){this.idx=e}isAtEnd(){return"eof"===(this.idx<this.len?this.tokens[this.idx]:this.eof).kind}},de=/^(PEPTIDE|RNA|DNA|CHEM|BLOB|G)([0-9]+)$/;function ce(e){let t=de.exec(e);if(null===t)return null;let i=t[1],n=parseInt(t[2],10);switch(i){case"PEPTIDE":return{rawTypeName:"PEPTIDE",polymerType:B.PEPTIDE,number:n,isDnaShim:!1,isGroup:!1};case"RNA":return{rawTypeName:"RNA",polymerType:B.RNA,number:n,isDnaShim:!1,isGroup:!1};case"DNA":return{rawTypeName:"DNA",polymerType:B.RNA,number:n,isDnaShim:!0,isGroup:!1};case"CHEM":return{rawTypeName:"CHEM",polymerType:B.CHEM,number:n,isDnaShim:!1,isGroup:!1};case"BLOB":return{rawTypeName:"BLOB",polymerType:B.BLOB,number:n,isDnaShim:!1,isGroup:!1};case"G":return{rawTypeName:"G",polymerType:B.PEPTIDE,number:n,isDnaShim:!1,isGroup:!0};default:return null}}var ue=class{constructor(e,t,i){this.diagnostics=[],this.chains=[],this.chainById=new Map,this.pendingBonds=[],this.groups=[],this.atomIds=new S,this.bondIds=new S,this.cursor=new he(e),this.source=e.source,this.lib=t,this.mode=i,this.annotations={perPolymer:new Map,version:""}}parseDocument(){if(this.cursor.isAtEnd())return this.emit("warning","empty-helm","Empty HELM string"),{mol:b(),diagnostics:this.diagnostics};if(this.parseSimplePolymers(),this.expectDollarSeparator(1),this.parseConnections(),this.expectDollarSeparator(2),this.parseGroupsSection(),this.expectDollarSeparator(3),this.parseAnnotationsSection(),this.cursor.at("dollar")&&(this.cursor.advance(),this.parseVersionTrailer()),!this.cursor.isAtEnd())for(this.emit("warning","extra-section-separator","Unexpected trailing tokens after HELM document",this.cursor.currentSpan());!this.cursor.isAtEnd();)this.cursor.advance();return{mol:this.finalize(),diagnostics:this.diagnostics}}expectDollarSeparator(e){this.cursor.at("dollar")?this.cursor.advance():this.emit("error","missing-section-separator",`Expected '$' separator before section ${e+1}`,this.cursor.currentSpan())}parseSimplePolymers(){if(!this.cursor.at("dollar")&&!this.cursor.isAtEnd())for(this.parsePolymer();this.cursor.at("pipe");){if(this.cursor.advance(),this.cursor.at("dollar")||this.cursor.isAtEnd())return void this.emit("warning","empty-polymer-body","Empty polymer after '|'",this.cursor.currentSpan());this.parsePolymer()}}parsePolymer(){let e=this.cursor.currentSpan(),t=this.cursor.optional("identifier");if(null===t)return this.emit("error","unexpected-token",`Expected polymer id, got '${this.cursor.peek().value}'`,this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let i=ce(t.value);if(null===i)return this.emit("error","unknown-polymer-type",`Unknown polymer type '${t.value}'`,t.span),void this.skipUntil(["pipe","dollar","eof"]);if(this.chainById.has(t.value)&&this.emit("warning","duplicate-polymer-id",`Duplicate polymer id '${t.value}'`,t.span),null===this.cursor.optional("lbrace"))return void this.emit("error","unexpected-token",`Expected '{' after polymer id '${t.value}'`,this.cursor.currentSpan());let n={id:t.value,polymerType:i.polymerType,rawTypeName:i.rawTypeName,rawNumber:i.number,backboneAtoms:[],allAtoms:[],bonds:[],span:{start:e.start,end:e.end}};if(this.chains.push(n),this.chainById.set(n.id,n),this.cursor.at("rbrace"))this.emit("warning","empty-polymer-body",`Empty body for polymer '${n.id}'`,this.cursor.currentSpan());else if(i.isGroup)this.parseGroupBody(n);else switch(i.polymerType){case B.PEPTIDE:this.parsePeptideBody(n);break;case B.RNA:this.parseRnaBody(n,i.isDnaShim),i.isDnaShim&&this.emit("info","dna-emitted-as-rna",`DNA polymer '${n.id}' will be emitted as RNA on canonicalize`,t.span);break;case B.CHEM:this.parseChemBody(n);break;case B.BLOB:this.parseBlobBody(n)}if(null===this.cursor.optional("rbrace"))return this.emit("error","unterminated-brace",`Expected '}' to close polymer '${n.id}'`,this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let o=this.cursor.optional("quote-string");null!==o&&(n.annotation=o.value)}parsePeptideBody(e){for(this.parsePeptideItem(e);this.cursor.at("dot")&&(this.cursor.advance(),!this.cursor.at("rbrace")&&!this.cursor.at("gt"));)this.parsePeptideItem(e);if(this.cursor.at("gt")){let t=this.cursor.currentSpan();this.cursor.advance(),this.emit("warning","peptide-cyclic-without-closure",`Peptide '${e.id}' marked cyclic with '>' — no explicit closure connection emitted`,t)}}parsePeptideItem(e){if(this.cursor.at("lparen"))this.parsePeptideAlternation(e);else{let t=this.parsePeptideAtom(e);this.maybeRepeatBracket(e,[t])}this.maybeAttachAnnotation(e)}parsePeptideAtom(e){let t=this.consumeMonomerSymbol(!1),{symbol:i,annotation:n,ambiguity:o,ambiguityKind:r,isInlineSmiles:s,rawPayload:a,inlineSource:l,span:h}=t,d=this.makeAtom(e,y,i);void 0!==n&&(d.tag=n),void 0!==o&&(d.bio.ambiguity=o),void 0!==r&&(d.bio.ambiguityKind=r),void 0!==l&&(d.inlineSource=l),s&&this.registerInlineSmiles(a,h,B.PEPTIDE),this.addToChain(e,d,!0);let c=e.backboneAtoms[e.backboneAtoms.length-2];return void 0!==c&&this.addBond(e,c,d,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1}),d}parsePeptideAlternation(e){let t=this.cursor.currentSpan();if(this.cursor.advance(),this.peptideContentIsSubsequence()){let t=e.backboneAtoms.length;for(this.parsePeptideItem(e);this.cursor.at("dot")&&(this.cursor.advance(),!this.cursor.at("rparen")&&!this.cursor.isAtEnd());)this.parsePeptideItem(e);null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' to close repeat sub-sequence",this.cursor.currentSpan());let i=e.backboneAtoms.slice(t);return this.maybeRepeatBracket(e,i),void this.maybeAttachAnnotation(e)}let i=[],n=null;for(;!this.cursor.at("rparen")&&!this.cursor.isAtEnd();){let e=this.parseAlternationCandidate(B.PEPTIDE);if(i.push(e),this.cursor.at("comma"))"and"===n&&this.emit("warning","mixed-separator-in-alternation","Mixed ',' and '+' separators in alternation",this.cursor.currentSpan()),n="or",this.cursor.advance();else{if(!this.cursor.at("plus"))break;"or"===n&&this.emit("warning","mixed-separator-in-alternation","Mixed ',' and '+' separators in alternation",this.cursor.currentSpan()),n="and",this.cursor.advance()}}null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' to close alternation",this.cursor.currentSpan());let o="and"===n?"+":",",r=`(${i.map(e=>e.symbol+(void 0!==e.ratio?`:${String(e.ratio)}`:"")).join(o)})`,s=this.makeAtom(e,y,"?");s.bio.ambiguity=r,s.bio.ambiguityKind="and"===n?"and":"or",this.addToChain(e,s,!0);let a=e.backboneAtoms[e.backboneAtoms.length-2];if(void 0!==a&&this.addBond(e,a,s,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1}),"and"===n)for(let e of i)"number"==typeof e.ratio&&e.ratio<0&&this.emit("error","ratio-and-negative",`Negative ratio ${e.ratio} in AND mixture`,t);this.maybeRepeatBracket(e,[s]),this.maybeAttachAnnotation(e)}peptideContentIsSubsequence(){let e=1,t=0;for(;;){let i=this.cursor.peek(t);if("eof"===i.kind)return!1;if("lparen"!==i.kind)if("rparen"!==i.kind){if(1===e){if("dot"===i.kind)return!0;if("comma"===i.kind||"plus"===i.kind||"colon"===i.kind)return!1}if(t+=1,t>1024)return!1}else{if(e-=1,0===e)return!0;t+=1}else e+=1,t+=1}}parseAlternationCandidate(e){let t,{symbol:i,isInlineSmiles:n,rawPayload:o,span:r}=this.consumeMonomerSymbol(!0);if(n&&this.registerInlineSmiles(o,r,e),null!==this.cursor.optional("colon")){let e=this.cursor.peek();"integer"===e.kind||"decimal"===e.kind?(this.cursor.advance(),t=parseFloat(e.value)):"question"===e.kind?(this.cursor.advance(),t="?"):this.emit("error","unexpected-token","Expected ratio after ':' in alternation",e.span)}return void 0===t?{symbol:i}:{symbol:i,ratio:t}}parseRnaBody(e,t){for(this.parseRnaItem(e,t);this.cursor.at("dot")&&(this.cursor.advance(),!(this.cursor.at("rbrace")||this.cursor.at("dollar")||this.cursor.isAtEnd()));)this.parseRnaItem(e,t)}parseRnaItem(e,t){if(this.cursor.at("lparen"))return void this.parseRnaAlternation(e,t);if(this.cursor.at("asterisk")){this.cursor.currentSpan(),this.cursor.advance();let t=this.makeAtom(e,E,"*");this.addToChain(e,t,!0);let i=e.backboneAtoms[e.backboneAtoms.length-2];return void 0!==i&&this.addBond(e,i,t,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1}),this.maybeRepeatBracket(e,[t]),void this.maybeAttachAnnotation(e)}let i,n,o=this.parseRnaSugar(e,t);this.maybeAttachAnnotation(e),this.cursor.at("lparen")&&(this.cursor.advance(),this.cursor.at("rparen")||(i=this.parseRnaBaseSymbol(e),this.maybeAttachAnnotationTo(i)),null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' after RNA base",this.cursor.currentSpan()),void 0!==i&&(this.addBond(e,o,i,"branch",{kind:"numeric",r:3},{kind:"numeric",r:1}),o.branchAtom=i)),this.canStartRnaLinker()&&(n=this.parseRnaLinker(e),this.maybeAttachAnnotationTo(n)),void 0!==n&&this.addBond(e,o,n,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1});let r=e.backboneAtoms.indexOf(o);if(r>0){let t=e.backboneAtoms[r-1];this.addBond(e,t,o,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1})}let s=[o];void 0!==i&&s.push(i),void 0!==n&&s.push(n),this.maybeRepeatBracket(e,s)}canStartRnaLinker(){let e=this.cursor.peek().kind;return"identifier"===e||"inline-smiles"===e||"asterisk"===e}parseRnaSugar(e,t){let{symbol:i,isInlineSmiles:n,rawPayload:o,inlineSource:r,span:s}=this.consumeMonomerSymbol(!1),a=this.makeAtom(e,v,i);return void 0!==r&&(a.inlineSource=r),n&&this.registerInlineSmiles(o,s,B.RNA),this.addToChain(e,a,!0),a}parseRnaBaseSymbol(e){let{symbol:t,isInlineSmiles:i,rawPayload:n,inlineSource:o,span:r}=this.consumeMonomerSymbol(!1),s=this.makeAtom(e,w,t);return void 0!==o&&(s.inlineSource=o),i&&this.registerInlineSmiles(n,r,B.RNA),this.addToChain(e,s,!1),s}parseRnaLinker(e){if(this.cursor.at("asterisk")){this.cursor.currentSpan(),this.cursor.advance();let t=this.makeAtom(e,x,"*");return this.addToChain(e,t,!0),t}let{symbol:t,isInlineSmiles:i,rawPayload:n,inlineSource:o,span:r}=this.consumeMonomerSymbol(!1),s=this.makeAtom(e,x,t);return void 0!==o&&(s.inlineSource=o),i&&this.registerInlineSmiles(n,r,B.RNA),this.addToChain(e,s,!0),s}parseRnaAlternation(e,t){let i=e.backboneAtoms.length;if(this.cursor.advance(),this.looksLikeFlatAlternation()){let t=[],i=null;for(;!this.cursor.at("rparen")&&!this.cursor.isAtEnd();)if(t.push(this.parseAlternationCandidate(B.RNA)),this.cursor.at("comma"))i="or",this.cursor.advance();else{if(!this.cursor.at("plus"))break;i="and",this.cursor.advance()}null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' in RNA alternation",this.cursor.currentSpan());let n="and"===i?"+":",",o=`(${t.map(e=>e.symbol+(void 0!==e.ratio?`:${String(e.ratio)}`:"")).join(n)})`,r=this.makeAtom(e,w,"?");r.bio.ambiguity=o,r.bio.ambiguityKind="and"===i?"and":"or",this.addToChain(e,r,!0);let s=e.backboneAtoms[e.backboneAtoms.length-2];return void 0!==s&&this.addBond(e,s,r,"backbone",{kind:"numeric",r:2},{kind:"numeric",r:1}),this.maybeRepeatBracket(e,[r]),void this.maybeAttachAnnotation(e)}for(this.parseRnaItem(e,t);this.cursor.at("dot")&&(this.cursor.advance(),!this.cursor.at("rparen")&&!this.cursor.isAtEnd());)this.parseRnaItem(e,t);null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' in RNA repeat",this.cursor.currentSpan());let n=e.backboneAtoms.slice(i);this.maybeRepeatBracket(e,n),this.maybeAttachAnnotation(e)}looksLikeFlatAlternation(){let e=1,t=0,i=!1;for(;;){let n=this.cursor.peek(t);if("eof"===n.kind)return i;if("rparen"===n.kind){if(e-=1,0===e)return i}else{if("lparen"===n.kind)return!1;if("dot"===n.kind)return!1;1===e&&("comma"===n.kind||"plus"===n.kind)&&(i=!0)}if(t+=1,t>256)return i}}parseChemBody(e){let t;if(this.cursor.at("asterisk"))this.cursor.advance(),t=this.makeAtom(e,C,"*"),this.addToChain(e,t,!0);else{let{symbol:i,isInlineSmiles:n,rawPayload:o,inlineSource:r,span:s}=this.consumeMonomerSymbol(!1);t=this.makeAtom(e,C,i),void 0!==r&&(t.inlineSource=r),n&&this.registerInlineSmiles(o,s,B.CHEM),this.addToChain(e,t,!0)}this.maybeAttachAnnotation(e),this.cursor.at("apos")&&this.maybeRepeatBracket(e,[t]),this.cursor.at("rbrace")||(this.emit("error","chem-multiple-monomers",`CHEM polymer '${e.id}' must contain exactly one monomer`,this.cursor.currentSpan()),this.skipUntil(["rbrace","eof"]))}parseBlobBody(e){let t,i,n,o=!1,r="",s=this.cursor.currentSpan();if(this.cursor.at("inline-smiles")){let e=this.cursor.advance();o=T(e.value),r=e.value,t=e.value,i=e.value,n=e.value,s=e.span}else if(this.cursor.at("identifier")){let e=this.cursor.advance();t=e.value,i=e.value,s=e.span}else this.emit("error","unknown-blobtype","Expected BLOB identifier",this.cursor.currentSpan()),t="?",i="?";let a=this.makeAtom(e,k,t);a.bio.blobtype=i,void 0!==n&&(a.inlineSource=n),o&&this.registerInlineSmiles(r,s,B.BLOB),this.addToChain(e,a,!0),this.maybeAttachAnnotation(e)}parseGroupBody(e){let t=0;for(;;){let e=this.cursor.peek();if("eof"===e.kind||0===t&&"rbrace"===e.kind)break;"lbrace"===e.kind&&(t+=1),"rbrace"===e.kind&&(t-=1),this.cursor.advance()}}parseConnections(){if(!this.cursor.at("dollar")&&!this.cursor.isAtEnd())for(this.parseConnection();this.cursor.at("pipe")&&(this.cursor.advance(),!this.cursor.at("dollar")&&!this.cursor.isAtEnd());)this.parseConnection()}parseConnection(){let e=this.cursor.currentSpan(),t=this.cursor.optional("identifier");if(null===t)return this.emit("error","unexpected-token","Expected chain id in connection",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);if(null===this.cursor.optional("comma"))return this.emit("error","unexpected-token","Expected ',' in connection",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let i=this.cursor.optional("identifier");if(null===i)return this.emit("error","unexpected-token","Expected second chain id in connection",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);if(null===this.cursor.optional("comma"))return this.emit("error","unexpected-token","Expected ',' before connection position",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let n=this.parsePosition();if(null===this.cursor.optional("colon"))return this.emit("error","unexpected-token","Expected ':' between position and R-group",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let o=this.parseRGroupSpec();if(null===this.cursor.optional("dash"))return this.emit("error","unexpected-token","Expected '-' between connection endpoints",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let r=this.parsePosition();if(null===this.cursor.optional("colon"))return this.emit("error","unexpected-token","Expected ':' before second R-group",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let s=this.parseRGroupSpec(),a=this.cursor.optional("quote-string"),l="pair"===o.kind&&"pair"===s.kind?"hbond":"cross-polymer",h={chain1:t.value,pos1:n,r1:o,chain2:i.value,pos2:r,r2:s,kind:l,span:{start:e.start,end:a?.span.end??this.cursor.peek().span.start},...null!==a?{tag:a.value}:{}};this.pendingBonds.push(h)}parsePosition(){let e=this.cursor.peek();return"integer"===e.kind?(this.cursor.advance(),{kind:"index",value:parseInt(e.value,10)}):"question"===e.kind?(this.cursor.advance(),{kind:"any"}):"identifier"===e.kind?(this.cursor.advance(),this.emit("info","symbol-position-reference",`Connection position uses monomer symbol '${e.value}' as chain-level ambiguity`,e.span),{kind:"symbol",value:e.value}):(this.emit("error","invalid-position",`Expected position (integer, '?', or symbol), got '${e.value}'`,e.span),{kind:"any"})}parseRGroupSpec(){let e=this.cursor.peek();if("question"===e.kind)return this.cursor.advance(),{kind:"unspecified"};if("asterisk"===e.kind)return this.cursor.advance(),{kind:"wildcard"};if("identifier"===e.kind){if(this.cursor.advance(),"pair"===e.value)return{kind:"pair"};let t=/^R([1-9][0-9]*)$/.exec(e.value);return null===t?(this.emit("error","invalid-rgroup",`Expected R-group label, got '${e.value}'`,e.span),{kind:"unspecified"}):{kind:"numeric",r:parseInt(t[1],10)}}return this.emit("error","invalid-rgroup",`Expected R-group label, got '${e.value}'`,e.span),{kind:"unspecified"}}parseGroupsSection(){if(!this.cursor.at("dollar")&&!this.cursor.isAtEnd())for(this.parseGroupOrBondRatio();this.cursor.at("pipe")&&(this.cursor.advance(),!this.cursor.at("dollar")&&!this.cursor.isAtEnd());)this.parseGroupOrBondRatio()}parseGroupOrBondRatio(){let e=this.cursor.optional("identifier");if(null===e)return this.emit("error","unexpected-token","Expected group or bond-ratio identifier",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);this.cursor.at("lparen")?this.parseGroupAfterId(e):this.cursor.at("plus")?this.parseBondRatioAfterId(e):(this.emit("warning","unexpected-token",`Expected '(' or '+' after id '${e.value}' in section 3`,this.cursor.currentSpan()),this.skipUntil(["pipe","dollar","eof"]))}parseGroupAfterId(e){let t=ce(e.value);(null===t||!t.isGroup)&&this.emit("error","unknown-group-reference",`Group id must be 'G<n>', got '${e.value}'`,e.span),this.cursor.advance();let i=[],n="or",o=null;for(;!this.cursor.at("rparen")&&!this.cursor.isAtEnd();){let e=this.parseGroupMember();if(null!==e&&i.push(e),this.cursor.at("comma"))null===o&&(o="or",n="or"),this.cursor.advance();else{if(!this.cursor.at("plus"))break;null===o&&(o="and",n="and"),this.cursor.advance()}}null===this.cursor.optional("rparen")&&this.emit("error","unterminated-paren","Expected ')' to close group",this.cursor.currentSpan()),this.groups.push({id:e.value,kind:n,members:i})}parseGroupMember(){let e,t=this.cursor.optional("identifier");return null===t?(this.emit("error","unexpected-token","Expected group member id",this.cursor.currentSpan()),null):(null!==this.cursor.optional("colon")&&(e=this.parseRatio()),void 0===e?{target:t.value}:{target:t.value,ratio:e})}parseRatio(){let e=this.cursor.peek();if("integer"===e.kind||"decimal"===e.kind){this.cursor.advance();let t=parseFloat(e.value);if(this.cursor.at("dash")&&(this.cursor.peek(),"integer"===this.cursor.peek(1).kind)){this.cursor.advance();let t=this.cursor.advance();this.emit("info","ratio-range",`Ratio range ${e.value}-${t.value}; using lower bound`,{start:e.span.start,end:t.span.end})}return t}return"question"===e.kind?(this.cursor.advance(),"?"):(this.emit("error","unexpected-token",`Expected ratio after ':', got '${e.value}'`,e.span),0)}parseBondRatioAfterId(e){this.cursor.advance();let t,i=this.cursor.optional("identifier");if(null===i)return void this.emit("error","unexpected-token","Expected second chain id in bond-ratio",this.cursor.currentSpan());if(null!==this.cursor.optional("colon")){let e=this.parseRatio();"number"==typeof e&&(t=e)}let n=this.pendingBonds.find(t=>t.chain1===e.value&&t.chain2===i.value||t.chain1===i.value&&t.chain2===e.value);void 0!==n?void 0!==t&&(n.ratio={numerator:t}):this.emit("warning","bond-ratio-no-matching-bond",`Bond-ratio for ${e.value}+${i.value} has no matching cross-polymer bond`,e.span)}parseAnnotationsSection(){if(!this.cursor.at("dollar")&&!this.cursor.isAtEnd()){if(this.cursor.position(),this.cursor.at("lbrace"))return this.parseAnnotation20(),void(this.cursor.at("pipe")&&(this.emit("info","annotation-mixed-versions","Mixed HELM 2.0 JSON and HELM 1.0 pipe annotations",this.cursor.currentSpan()),this.cursor.advance(),this.parseAnnotation10Entries()));this.parseAnnotation10Entries()}}parseAnnotation20(){let e=this.cursor.currentSpan(),t=0,i=e.end;for(;!this.cursor.isAtEnd();){let e=this.cursor.peek();if("lbrace"===e.kind)t+=1;else if("rbrace"===e.kind&&(t-=1,0===t)){i=e.span.end,this.cursor.advance();break}this.cursor.advance()}let n=this.source.slice(e.start,i),o=null;try{o=JSON.parse(n)}catch{return this.emit("warning","annotation-malformed-json","Annotation block is not valid JSON",{start:e.start,end:i}),void(this.annotations={perPolymer:this.annotations.perPolymer,version:this.annotations.version,raw:n})}if(null===o||"object"!=typeof o||Array.isArray(o))this.emit("warning","annotation-malformed-json","Annotation block parsed but is not an object",{start:e.start,end:i}),this.annotations={perPolymer:this.annotations.perPolymer,version:this.annotations.version,raw:n};else{let t=new Map(this.annotations.perPolymer);for(let[i,n]of Object.entries(o))null===n||"object"!=typeof n||Array.isArray(n)?t.set(i,{value:n}):(t.set(i,{...n}),this.chainById.has(i)||this.emit("warning","annotation-unknown-polymer",`Annotation references unknown polymer '${i}'`,e));this.annotations={perPolymer:t,version:this.annotations.version}}}parseAnnotation10Entries(){for(this.parseAnnotation10One();this.cursor.at("pipe")&&(this.cursor.advance(),!this.cursor.at("dollar")&&!this.cursor.isAtEnd());)this.parseAnnotation10One()}parseAnnotation10One(){let e=this.cursor.optional("identifier");if(null===e)return this.emit("warning","annotation-malformed-json","Expected polymer-id in HELM 1.0 annotation",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);if(null===this.cursor.optional("lbrace"))return this.emit("warning","annotation-malformed-json","Expected '{' after polymer-id",this.cursor.currentSpan()),void this.skipUntil(["pipe","dollar","eof"]);let t=[];for(;!this.cursor.at("rbrace")&&!this.cursor.isAtEnd();)t.push(this.cursor.advance().value);if(null===this.cursor.optional("rbrace"))return void this.emit("error","unterminated-brace","Expected '}' to close annotation",this.cursor.currentSpan());let i=t.join("").trim(),n=new Map(this.annotations.perPolymer),o=n.get(e.value)??{};"ss"===i||"as"===i?n.set(e.value,{...o,strandtype:i}):n.set(e.value,{...o,[i]:!0}),this.chainById.has(e.value)||this.emit("warning","annotation-unknown-polymer",`Annotation references unknown polymer '${e.value}'`,e.span),this.annotations={perPolymer:n,version:this.annotations.version}}parseVersionTrailer(){let e=this.cursor.optional("identifier");if(null===e)return void(this.annotations={...this.annotations,version:""});let t=e.value;if(this.cursor.at("dot")&&"integer"===this.cursor.peek(1).kind){this.cursor.advance();let i=this.cursor.advance();t=`${e.value}.${i.value}`}this.annotations={...this.annotations,version:t}}skipUntil(e){for(;!this.cursor.isAtEnd();){if(e.includes(this.cursor.peek().kind))return;this.cursor.advance()}}consumeMonomerSymbol(e){let t=this.cursor.peek();if("inline-smiles"===t.kind){this.cursor.advance();let e=T(t.value);return{symbol:t.value,isInlineSmiles:e,rawPayload:t.value,inlineSource:t.value,span:t.span}}if("identifier"===t.kind){this.cursor.advance();let e=t.value,i=t.span;for(;"dash"===this.cursor.peek().kind&&"integer"===this.cursor.peek(1).kind&&("identifier"===this.cursor.peek(2).kind||"dash"===this.cursor.peek(2).kind);){this.cursor.advance();let t=this.cursor.advance();if(e=`${e}-${t.value}`,i=t.span,"identifier"===this.cursor.peek().kind){let t=this.cursor.advance();e=`${e}${t.value}`,i=t.span}}return{symbol:e,isInlineSmiles:!1,rawPayload:e,span:{start:t.span.start,end:i.end}}}if("asterisk"===t.kind||"underscore"===t.kind||"question"===t.kind)return this.cursor.advance(),{symbol:t.value,isInlineSmiles:!1,rawPayload:t.value,span:t.span};if("integer"===t.kind&&"identifier"===this.cursor.peek(1).kind){let e=this.cursor.advance(),t=this.cursor.advance(),i=`${e.value}${t.value}`;return{symbol:i,isInlineSmiles:!1,rawPayload:i,span:{start:e.span.start,end:t.span.end}}}return this.emit("error","unexpected-token",`Expected monomer symbol, got '${t.value}'`,t.span),{symbol:"?",isInlineSmiles:!1,rawPayload:"",span:t.span}}maybeRepeatBracket(e,t){if(!this.cursor.at("apos"))return;let i=this.cursor.currentSpan();this.cursor.advance();let n=this.cursor.optional("integer");if(null===n)return this.emit("error","unexpected-token","Expected integer in repeat bracket",this.cursor.currentSpan()),void this.cursor.optional("apos");let o=parseInt(n.value,10),r=o;if(this.cursor.at("dash")){this.cursor.advance();let e=this.cursor.optional("integer");null===e?this.emit("error","unexpected-token","Expected integer after '-' in repeat bracket",this.cursor.currentSpan()):r=parseInt(e.value,10)}if(null===this.cursor.optional("apos")&&this.emit("error","unterminated-apostrophe","Expected closing apostrophe",this.cursor.currentSpan()),0!==t.length){if(r<o){this.emit("warning","repeat-range-inverted",`Repeat range ${o}-${r} has max < min; swapping`,i);let e=o;o=r,r=e}0!==o||0!==r?(r>1e4&&this.emit("warning","bracket-repeat-too-large",`Repeat range upper bound ${r} > 10000`,i),e.polymerType===B.CHEM&&this.emit("error","repeat-on-non-iterable-polymer",`Repeat bracket not allowed on CHEM polymer '${e.id}'`,i),this.groups.push({id:`${e.id}/bracket@${t[0]?.id??0}`,kind:"bracket",members:t.map(e=>({target:String(e.id)})),repeat:{min:o,max:r}})):this.emit("warning","repeat-zero-count","Repeat bracket with zero count",i)}else this.emit("warning","repeat-on-empty-bracket","Repeat bracket applied to empty content",i)}maybeAttachAnnotation(e){let t=e.backboneAtoms[e.backboneAtoms.length-1];void 0!==t&&this.maybeAttachAnnotationTo(t)}maybeAttachAnnotationTo(e){if(void 0===e)return;let t=this.cursor.optional("quote-string");null!==t&&(e.tag=t.value)}registerInlineSmiles(e,t,i){if(T(e)){if(null===this.lib)return void this.emit("info","inline-smiles-no-lib","Inline SMILES seen but no monomer library available for registration",t);try{this.lib.addMonomer;let t=this.lib.registerInlineSmilesMonomer;"function"==typeof t&&t.call(this.lib,i,e)}catch(e){let i=e instanceof Error?e.message:String(e);this.emit("warning","inline-smiles-without-r-groups",`Inline SMILES registration failed: ${i}`,t)}}}makeAtom(e,t,i){return{id:this.atomIds.next(),p:{x:0,y:0},biotype:t,symbol:i,monomer:null,bio:{chainId:e.id,positionInChain:0,continuousId:0},hidden:!1,selected:!1,highlighted:!1}}addToChain(e,t,i){e.allAtoms.push(t),i&&(e.backboneAtoms.push(t),t.bio.positionInChain=e.backboneAtoms.length)}addBond(e,t,i,n,o,r){let s=this.bondIds.next();e.bonds.push({id:s,a1:t,a2:i,kind:n,r1:o,r2:r})}finalize(){let e=[];for(let t of this.pendingBonds){let i=this.chainById.get(t.chain1),n=this.chainById.get(t.chain2);if(void 0===i){this.emit("error","unknown-chain-reference",`Connection references unknown chain '${t.chain1}'`,t.span);continue}if(void 0===n){this.emit("error","unknown-chain-reference",`Connection references unknown chain '${t.chain2}'`,t.span);continue}let o=this.resolveAtomByPosition(i,t.pos1,t.span),r=this.resolveAtomByPosition(n,t.pos2,t.span);if(null===o||null===r)continue;"pair"===t.r1.kind&&void 0!==o.branchAtom&&(o=o.branchAtom),"pair"===t.r2.kind&&void 0!==r.branchAtom&&(r=r.branchAtom);let s={id:this.bondIds.next(),a1:o,a2:r,kind:t.kind,r1:t.r1,r2:t.r2,...void 0!==t.tag?{tag:t.tag}:{},...void 0!==t.ratio?{ratio:t.ratio}:{}};e.push(s)}let t=[],i=[],n=[];for(let e of this.chains){for(let i of e.allAtoms)t.push(i);for(let t of e.bonds)i.push(t);let o=this.annotations.perPolymer.get(e.id),r=void 0===o?void 0:o.strandtype,s="ss"===r||"as"===r?r:void 0;n.push({id:e.id,polymerType:e.polymerType,backboneAtoms:e.backboneAtoms,bonds:e.bonds,...void 0!==e.annotation?{annotation:e.annotation}:{},...void 0!==s?{strandType:s}:{}})}for(let t of e)i.push(t);let o=0;for(let e of this.chains)for(let t of e.backboneAtoms)o+=1,t.bio.continuousId=o,void 0!==t.branchAtom&&(o+=1,t.branchAtom.bio.continuousId=o);let r=[];for(let e of this.groups)r.push({id:e.id,kind:e.kind,members:e.members,...void 0!==e.repeat?{repeat:e.repeat}:{}});return{atoms:t,bonds:i,chains:n,groups:r,annotations:this.annotations}}sourceOrderAtoms(e){let t=[];for(let i of e.backboneAtoms)t.push(i),void 0!==i.branchAtom&&t.push(i.branchAtom);return t}resolveAtomByPosition(e,t,i){if("any"===t.kind)return e.backboneAtoms[0]??null;if("symbol"===t.kind){let n=e.backboneAtoms.find(e=>e.symbol===t.value);if(void 0===n){let n=e.allAtoms.find(e=>e.symbol===t.value);return void 0===n?(this.emit("warning","position-out-of-range",`Chain '${e.id}' has no monomer with symbol '${t.value}'`,i),e.backboneAtoms[0]??null):n}return n}let n=this.sourceOrderAtoms(e),o=t.value;return o<1||o>n.length?(this.emit("error","position-out-of-range",`Position ${o} out of range for chain '${e.id}' (length ${n.length})`,i),e.backboneAtoms[0]??null):n[o-1]}emit(e,t,i,n){let o={severity:e,code:t,message:i,...void 0!==n?{span:{start:n.start,end:n.end}}:{}};if(this.diagnostics.push(o),"strict"===this.mode&&"error"===e)throw new r(t,i,{...void 0!==n?{span:{start:n.start,end:n.end}}:{}})}};function pe(e,t){let i=function(e){let t=(t,i)=>t.polymerType===B.CHEM||t.polymerType===B.BLOB||!function(e,t,i){for(let n of i){if("backbone"!==n.kind||"numeric"!==n.r1.kind||"numeric"!==n.r2.kind)continue;let i=n.a1.id===e.id&&n.a2.id===t.id&&2===n.r1.r&&1===n.r2.r,o=n.a1.id===t.id&&n.a2.id===e.id&&2===n.r1.r&&1===n.r2.r;if(i||o)return!0}return!1}(t.backboneAtoms[i],t.backboneAtoms[i+1],e.bonds),i=!1;for(let n of e.chains){for(let e=0;e<n.backboneAtoms.length-1;e++)if(t(n,e)){i=!0;break}if(i)break}if(!i)return e;let n=new Set(e.chains.map(e=>e.id)),o=e=>{let t=1;for(;n.has(`${e}${t}`);)t+=1;let i=`${e}${t}`;return n.add(i),i},r=[];for(let i of e.chains){let e=[[]],n=e[0];for(let o=0;o<i.backboneAtoms.length;o++){let r=i.backboneAtoms[o];n.push(r),o<i.backboneAtoms.length-1&&t(i,o)&&(n=[],e.push(n))}for(let t=0;t<e.length;t++){let n={id:0===t?i.id:o(i.polymerType),polymerType:i.polymerType,atoms:e[t]};0===t&&void 0!==i.annotation&&(n.annotation=i.annotation),r.push(n)}}let s=new Map;for(let e of r)for(let t=0;t<e.atoms.length;t++){let i=e.atoms[t];s.set(i.id,{chainId:e.id,pos:t+1}),void 0!==i.branchAtom&&s.set(i.branchAtom.id,{chainId:e.id,pos:t+1})}let a=new Map;for(let t of e.atoms){let e=s.get(t.id);void 0===e||t.bio.chainId===e.chainId&&t.bio.positionInChain===e.pos?a.set(t.id,t):a.set(t.id,{...t,bio:{...t.bio,chainId:e.chainId,positionInChain:e.pos}})}for(let t of e.atoms){if(void 0===t.branchAtom)continue;let e=a.get(t.id),i=a.get(t.branchAtom.id);void 0===e||void 0===i||(e.branchAtom=i)}let l=e.bonds.map(e=>{let t=a.get(e.a1.id)??e.a1,i=a.get(e.a2.id)??e.a2;return t===e.a1&&i===e.a2?e:{...e,a1:t,a2:i}}),h=r.map(e=>{let t=e.atoms.map(e=>a.get(e.id)??e),i=new Set;for(let t of e.atoms)i.add(t.id),void 0!==t.branchAtom&&i.add(t.branchAtom.id);let n=[];for(let e of l)i.has(e.a1.id)&&i.has(e.a2.id)&&n.push(e);return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:n,...void 0!==e.annotation?{annotation:e.annotation}:{}}});return{atoms:e.atoms.map(e=>a.get(e.id)??e),bonds:l,chains:h,groups:e.groups,annotations:e.annotations}}(e);return new me(i,t??{}).emit()}var me=class{constructor(e,t){this.mol=e,this.options=t}emit(){return`${this.orderedChains().map(e=>this.emitPolymer(e)).join("|")}$${this.emitConnections()}$${this.emitGroupsAndBondRatios()}$${this.emitAnnotations()}${this.versionTrailer()}`}orderedChains(){if(!0!==this.options.canonicalize)return this.mol.chains;let e=this.mol.chains.slice();return e.sort((e,t)=>e.polymerType!==t.polymerType?e.polymerType<t.polymerType?-1:1:e.id<t.id?-1:e.id>t.id?1:0),e}emitPolymer(e){let t=this.emitChainBody(e),i=void 0!==e.annotation?`"${fe(e.annotation)}"`:"";return`${e.id}{${t}}${i}`}emitChainBody(e){switch(e.polymerType){case"PEPTIDE":return this.emitPeptideBody(e);case"RNA":return this.emitRnaBody(e);case"CHEM":return this.emitChemBody(e);case"BLOB":return this.emitBlobBody(e);default:return""}}emitPeptideBody(e){let t=this.bracketsForChain(e.id),i=[],n=0,o=0,r=null;for(;n<e.backboneAtoms.length;){let s=e.backboneAtoms[n],a=t.find(e=>e.startAtomId===s.id);void 0!==a&&null===r&&(i.push("("),r=a,o+=1),i.push(this.emitMonomerToken(s));let l=void 0!==s.tag?`"${fe(s.tag)}"`:"";i.push(l),null!==r&&r.endAtomId===s.id&&(i.push(`)${be(r.min,r.max)}`),r=null,o-=1),n+=1,n<e.backboneAtoms.length&&i.push(".")}return i.join("")}emitRnaBody(e){let t=this.bracketsForChain(e.id),i=[],n=0,o=!0,r=null,s=e=>{null!==r&&r.endAtomId===e&&(i.push(`)${be(r.min,r.max)}`),r=null)},a=e=>{let n=t.find(t=>t.startAtomId===e);void 0!==n&&null===r&&(i.push("("),r=n)};for(;n<e.backboneAtoms.length;){let t=e.backboneAtoms[n];if(o||i.push("."),o=!1,t.biotype!==E){if(t.biotype===v){a(t.id),i.push(this.emitMonomerToken(t)),void 0!==t.tag&&i.push(`"${fe(t.tag)}"`),void 0!==t.branchAtom&&(i.push("("),i.push(this.emitMonomerToken(t.branchAtom)),void 0!==t.branchAtom.tag&&i.push(`"${fe(t.branchAtom.tag)}"`),i.push(")"));let o=e.backboneAtoms[n+1];void 0!==o&&o.biotype===x?(i.push(this.emitMonomerToken(o)),void 0!==o.tag&&i.push(`"${fe(o.tag)}"`),s(o.id),n+=2):(s(t.id),n+=1);continue}a(t.id),i.push(this.emitMonomerToken(t)),void 0!==t.tag&&i.push(`"${fe(t.tag)}"`),s(t.id),n+=1}else a(t.id),i.push(this.emitMonomerToken(t)),void 0!==t.tag&&i.push(`"${fe(t.tag)}"`),s(t.id),n+=1}return i.join("")}emitChemBody(e){let t=e.backboneAtoms[0];if(void 0===t)return"";let i=void 0!==t.tag?`"${fe(t.tag)}"`:"";return`${this.emitMonomerToken(t)}${i}`}emitBlobBody(e){let t=e.backboneAtoms[0];if(void 0===t)return"";let i=void 0!==t.tag?`"${fe(t.tag)}"`:"";return`${this.emitMonomerToken(t)}${i}`}emitMonomerToken(e){let t;return t=void 0!==e.inlineSource?`[${e.inlineSource}]`:void 0===e.bio.ambiguity||"?"!==e.symbol&&!e.bio.ambiguity.startsWith("(")?e.symbol:e.bio.ambiguity,!0===this.options.includeHighlights&&e.selected?`<span style='background:#bbf;'>${t}</span>`:t}emitConnections(){let e=[];for(let t of this.crossPolymerBonds())e.push(this.emitConnection(t));return e.join("|")}*crossPolymerBonds(){let e=new Map;for(let t of this.mol.chains){let i=new Map;for(let e=0;e<t.backboneAtoms.length;e++)i.set(t.backboneAtoms[e].id,e);e.set(t.id,i)}for(let t of this.mol.bonds)if("backbone"!==t.kind)if("branch"!==t.kind)yield t;else{if(void 0!==t.a1.branchAtom&&t.a1.branchAtom.id===t.a2.id||void 0!==t.a2.branchAtom&&t.a2.branchAtom.id===t.a1.id)continue;yield t}else{if(t.a1.bio.chainId===t.a2.bio.chainId){let i=e.get(t.a1.bio.chainId);if(void 0!==i){let e=i.get(t.a1.id),n=i.get(t.a2.id);if(void 0!==e&&void 0!==n&&1===Math.abs(e-n))continue}}yield t}}emitConnection(e){let t=ge(e.r1,e.kind),i=ge(e.r2,e.kind),n=void 0!==e.tag?`"${fe(e.tag)}"`:"",o=String(this.connectionPosition(e.a1)),r=String(this.connectionPosition(e.a2));return`${e.a1.bio.chainId},${e.a2.bio.chainId},${o}:${t}-${r}:${i}${n}`}connectionPosition(e){return _(e,this.mol.chains.find(t=>t.id===e.bio.chainId))}emitGroupsAndBondRatios(){let e=[];for(let t of this.mol.groups)"bracket"!==t.kind&&e.push(this.emitGroup(t));for(let t of this.mol.bonds){if("cross-polymer"!==t.kind||void 0===t.ratio)continue;let i=void 0!==t.ratio.denominator?`${t.ratio.numerator}/${t.ratio.denominator}`:`${t.ratio.numerator}`;e.push(`${t.a1.bio.chainId}+${t.a2.bio.chainId}:${i}`)}return e.join("|")}emitGroup(e){let t="and"===e.kind?"+":",",i=e.members.map(e=>{return void 0===(t=e).ratio?t.target:`${t.target}:${t.ratio}`;var t}).join(t);return`${e.id}(${i})`}emitAnnotations(){let e=this.mol.annotations.perPolymer;if(0===e.size)return"";let t={};for(let[i,n]of e)t[i]=n;return JSON.stringify(t)}versionTrailer(){let e=this.options.version??"V2.0";if("none"===e)return"";if("preserve"===e){let e=this.mol.annotations.version;return""===e?"":`$${e}`}return`$${e}`}bracketsForChain(e){let t=[],i=new Map;for(let e of this.mol.atoms)i.set(e.id,e.bio.chainId);for(let n of this.mol.groups){if("bracket"!==n.kind)continue;let o=[];for(let e of n.members){let t=parseInt(e.target,10);Number.isFinite(t)&&o.push(t)}if(0===o.length)continue;let r=new Set;for(let e of o){let t=i.get(e);void 0!==t&&r.add(t)}if(!r.has(e)||r.size>1)continue;let s=n.repeat??{min:1,max:1};t.push({members:o,min:s.min,max:s.max,set:new Set(o),startAtomId:o[0],endAtomId:o[o.length-1]})}return t}};function fe(e){let t="";for(let i=0;i<e.length;i++){let n=e.charCodeAt(i);t+=34!==n?92!==n?10!==n?13!==n?9!==n?e.charAt(i):"\\t":"\\r":"\\n":"\\\\":'\\"'}return t}function be(e,t){return e===t?`'${e}'`:`'${e}-${t}'`}function ge(e,t){switch(e.kind){case"numeric":return`R${e.r}`;case"unspecified":default:return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${e.position}:R${e.r}`}}var Ae=class{constructor(e){this.chainIdMap=new Map,this.mol=e}run(){let e=this.mol.chains.slice().sort((e,t)=>e.polymerType!==t.polymerType?e.polymerType<t.polymerType?-1:1:ve(e.id,t.id)),t={},i=[];for(let n of e){let e=_e(n.polymerType);t[e]=(t[e]??0)+1;let o=`${e}${t[e]}`;this.chainIdMap.set(n.id,o),i.push(n)}let n=new Map;for(let e of this.mol.atoms){let t=this.chainIdMap.get(e.bio.chainId)??e.bio.chainId;n.set(e.id,{...e,bio:{...e.bio,chainId:t}})}for(let e of this.mol.atoms){if(void 0===e.branchAtom)continue;let t=n.get(e.id),i=n.get(e.branchAtom.id);void 0!==t&&void 0!==i&&(t.branchAtom=i)}let o=this.mol.bonds.map(e=>({...e,a1:n.get(e.a1.id)??e.a1,a2:n.get(e.a2.id)??e.a2})),r=new Map;for(let e of o)r.set(e.id,e);let s=i.map(e=>{let t=this.chainIdMap.get(e.id)??e.id,i=[];for(let t of e.backboneAtoms){let e=n.get(t.id);void 0!==e&&i.push(e)}let o=[];for(let t of e.bonds){let e=r.get(t.id);void 0!==e&&o.push(e)}return{id:t,polymerType:e.polymerType,backboneAtoms:i,bonds:o,...void 0!==e.annotation&&e.annotation.length>0?{annotation:e.annotation}:{}}}),a=new Map;for(let e of s)a.set(e.id,e);o.sort((e,t)=>{let i=ye(e.kind),n=ye(t.kind);if(i&&!n)return 1;if(!i&&n)return-1;if(!i&&!n)return e.id-t.id;let o=e.a1.bio.chainId,r=t.a1.bio.chainId;if(o!==r)return o<r?-1:1;let s=e.a2.bio.chainId,l=t.a2.bio.chainId;if(s!==l)return s<l?-1:1;let h=_(e.a1,a.get(e.a1.bio.chainId)),d=_(t.a1,a.get(t.a1.bio.chainId));return h!==d?h-d:_(e.a2,a.get(e.a2.bio.chainId))-_(t.a2,a.get(t.a2.bio.chainId))});let l=this.renumberGroups(this.mol.groups),h=this.rekeyAnnotations(this.mol.annotations);return{atoms:this.mol.atoms.map(e=>n.get(e.id)),bonds:o,chains:s,groups:l,annotations:h}}renumberGroups(e){let t=[],i=[];for(let n of e)"bracket"===n.kind?t.push(this.rekeyBracket(n)):i.push(n);i.sort((e,t)=>ve(e.id,t.id));let n={G:0};return i.map(e=>{n.G+=1;let t=`G${n.G}`;return{...e,id:t,members:e.members.map(e=>this.rekeyMember(e))}}).concat(t)}rekeyBracket(e){return e}rekeyMember(e){let t=this.chainIdMap.get(e.target);return void 0===t?e:void 0===e.ratio?{target:t}:{target:t,ratio:e.ratio}}rekeyAnnotations(e){let t=new Map;for(let[i,n]of e.perPolymer){let e=this.chainIdMap.get(i)??i;0!==Object.keys(n).length&&t.set(e,n)}return{perPolymer:t,version:e.version}}};function _e(e){switch(e){case"PEPTIDE":return"PEPTIDE";case"RNA":return"RNA";case"CHEM":return"CHEM";default:return"BLOB"}}function ye(e){return"cross-polymer"===e||"hbond"===e}function ve(e,t){let i=/^([A-Z]+)([0-9]+)$/.exec(e),n=/^([A-Z]+)([0-9]+)$/.exec(t);return null===i||null===n?e<t?-1:e>t?1:0:i[1]!==n[1]?i[1]<n[1]?-1:1:parseInt(i[2],10)-parseInt(n[2],10)}function we(e,t){let i=[...e.atoms],n=i[0];for(let e of i)for(let i of t.get(e)??[])if("hbond"===i.kind)throw new a("gap-at-complex-junction",`Gap atom ${e} participates in a hydrogen bond`,{atomId:e});if(e.boundary.length>2)throw new a("gap-at-complex-junction",`Gap atom ${n} sits at a junction of ${e.boundary.length} connections (max 2 allowed)`,{atomId:n,bondCount:e.boundary.length});if(2===e.boundary.length){let t=xe(e,e.boundary[0]),i=xe(e,e.boundary[1]);if(t.atom.id===i.atom.id)throw new a("gap-at-complex-junction",`Removing gap atom ${n} would bond monomer '${t.atom.symbol}' to itself`,{atomId:n})}}function xe(e,t){return e.atoms.has(t.a1.id)?{atom:t.a2,r:t.r2}:{atom:t.a1,r:t.r1}}function Ce(e,t){return"numeric"===e.kind&&e.r===t}var ke=[function(e,t){let i=[],n=new Set(e.chains.map(e=>e.id));for(let t of e.bonds)"cross-polymer"!==t.kind&&"hbond"!==t.kind||(n.has(t.a1.bio.chainId)||i.push({severity:"error",code:"unknown-chain-reference",message:`Connection references unknown chain '${t.a1.bio.chainId}'`,context:{chainId:t.a1.bio.chainId,bondId:t.id}}),n.has(t.a2.bio.chainId)||i.push({severity:"error",code:"unknown-chain-reference",message:`Connection references unknown chain '${t.a2.bio.chainId}'`,context:{chainId:t.a2.bio.chainId,bondId:t.id}}));for(let t of e.chains)for(let n of e.bonds){if("cross-polymer"!==n.kind&&"hbond"!==n.kind)continue;let e=0;for(let i of t.backboneAtoms)e+=void 0!==i.branchAtom?2:1;for(let o of[n.a1,n.a2]){if(o.bio.chainId!==t.id)continue;let n=_(o,t);(n<1||n>e)&&i.push({severity:"error",code:"position-out-of-range",message:`Position ${n} out of range for chain '${t.id}' (length ${e})`,context:{chainId:t.id,atomId:o.id,found:n}})}}let o=new Set;for(let t of e.groups)"bracket"!==t.kind&&o.add(t.id);for(let t of e.groups)if("bracket"!==t.kind)for(let e of t.members)n.has(e.target)||o.has(e.target)||i.push({severity:"error",code:"unknown-group-reference",message:`Group '${t.id}' references unknown id '${e.target}'`,context:{found:e.target}});let r=new Map;for(let t of e.groups){if("bracket"===t.kind)continue;let e=[];for(let i of t.members)o.has(i.target)&&e.push(i.target);r.set(t.id,e)}for(let e of r.keys()){let t=new Set,n=[e];for(;n.length>0;){let o=n.pop();if(t.has(o))continue;t.add(o);let s=r.get(o)??[];for(let o of s)o===e?i.push({severity:"error",code:"group-cycle",message:`Group cycle detected involving '${e}'`,context:{found:e}}):t.has(o)||n.push(o)}}return i},function(e,t){let i=[];if(null===t)return i;let n=new Map;for(let t of e.chains)n.set(t.id,t.polymerType);for(let t of e.atoms){let e=n.get(t.bio.chainId);if(void 0===e)continue;let o=t.monomer,r=o?.meta;null!==o&&!0!==r?.missing?!0!==r?.ambiguous&&void 0!==o.smiles&&o.smiles.length>0&&(0===o.rgroups.length?i.push({severity:"warning",code:"inline-smiles-without-r-groups",message:`Inline-SMILES monomer '${o.symbol}' has no R-groups`,context:{atomId:t.id,found:o.symbol}}):o.rgroups.length>4&&i.push({severity:"warning",code:"inline-smiles-too-many-rs",message:`Inline-SMILES monomer '${o.symbol}' has ${o.rgroups.length} R-groups (max 4 expected)`,context:{atomId:t.id,found:o.rgroups.length}})):i.push({severity:"warning",code:"unresolved-monomer",message:`Monomer '${t.symbol}' not found in library for ${e}`,context:{chainId:t.bio.chainId,atomId:t.id,found:t.symbol}})}for(let o of e.atoms){let e=n.get(o.bio.chainId);if(void 0!==e&&null===t.getMonomer(e,o.symbol))for(let n of t.getMonomerSymbolsByType(e))if(n!==o.symbol&&n.toLowerCase()===o.symbol.toLowerCase()){i.push({severity:"info",code:"case-mismatch",message:`Symbol '${o.symbol}' differs from library entry '${n}' only in case`,context:{atomId:o.id,found:o.symbol,expected:n}});break}}return i},function(e,t){let i=[],n=new Map;for(let t of e.bonds)for(let[e,o]of[[t.a1,t.r1],[t.a2,t.r2]]){if("numeric"!==o.kind)continue;let r=n.get(e.id)??new Set;r.has(o.r)&&i.push({severity:"error",code:"rgroup-already-bonded",message:`R-group R${o.r} on atom ${e.id} already bonded`,context:{atomId:e.id,bondId:t.id,found:o.r}}),r.add(o.r),n.set(e.id,r)}for(let t of e.bonds){for(let[e,n]of[[t.a1,t.r1],[t.a2,t.r2]]){if("numeric"!==n.kind||null===e.monomer)continue;let o=e.monomer.rs;(n.r<1||n.r>o)&&i.push({severity:"error",code:"rgroup-not-on-monomer",message:`R-group R${n.r} not defined on monomer '${e.symbol}' (rs=${o})`,context:{atomId:e.id,bondId:t.id,found:n.r,expected:`R1..R${o}`}})}"backbone"===t.kind&&"numeric"===t.r1.kind&&"numeric"===t.r2.kind&&(2===t.r1.r&&1===t.r2.r||i.push({severity:"warning",code:"backbone-rgroup-misaligned",message:`Backbone bond uses R${t.r1.r}->R${t.r2.r} (expected R2->R1)`,context:{bondId:t.id,found:`R${t.r1.r}->R${t.r2.r}`}})),"branch"===t.kind&&"numeric"===t.r1.kind&&3!==t.r1.r&&i.push({severity:"warning",code:"branch-rgroup-misaligned",message:`Branch bond uses R${t.r1.r} (expected R3 on parent)`,context:{bondId:t.id,found:`R${t.r1.r}`}})}for(let t of e.atoms){if(null===t.monomer)continue;let e=n.get(t.id)?.size??0;if(t.monomer.rs>e){let n=t.monomer.rs-e;n>0&&t.monomer.rs>0&&i.push({severity:"info",code:"unmatched-r-group",message:`Monomer '${t.symbol}' on atom ${t.id} has ${n} unused R-group(s); default cap applied`,context:{atomId:t.id,found:n}})}}return i},function(e,t){let i=[];for(let t of e.chains){if("CHEM"===t.polymerType&&t.backboneAtoms.length>1&&i.push({severity:"error",code:"chem-multiple-monomers",message:`CHEM polymer '${t.id}' has ${t.backboneAtoms.length} monomers (expected 1)`,context:{chainId:t.id,found:t.backboneAtoms.length}}),"BLOB"===t.polymerType)for(let e of t.backboneAtoms)void 0===e.bio.blobtype&&"Bead"!==e.symbol&&"Group"!==e.symbol&&i.push({severity:"error",code:"blob-non-blob-symbol",message:`BLOB '${t.id}' contains non-blob symbol '${e.symbol}'`,context:{chainId:t.id,atomId:e.id,found:e.symbol}});if("RNA"===t.polymerType){let e=!1;for(let n=0;n<t.backboneAtoms.length;n++){let o=t.backboneAtoms[n];o.biotype===w&&!e&&i.push({severity:"error",code:"rna-bare-base",message:`Bare base '${o.symbol}' without parent sugar in '${t.id}'`,context:{chainId:t.id,atomId:o.id}}),o.biotype===x&&(t.backboneAtoms.slice(0,n).some(e=>e.biotype===v)||i.push({severity:"warning",code:"rna-bare-linker",message:`Bare linker '${o.symbol}' before any sugar in '${t.id}'`,context:{chainId:t.id,atomId:o.id}})),e=o.biotype===v||o.biotype===x}}}return i},function(e,t){let i=[],n=new Map;for(let t of e.chains)n.set(t.id,t.polymerType);let o=new Map;for(let t of e.bonds){if("hbond"!==t.kind)continue;o.set(t.a1.id,(o.get(t.a1.id)??0)+1),o.set(t.a2.id,(o.get(t.a2.id)??0)+1);let e=n.get(t.a1.bio.chainId),r=n.get(t.a2.bio.chainId);("RNA"!==e||"RNA"!==r)&&i.push({severity:"error",code:"pair-non-rna",message:`Hydrogen-bond connects non-RNA chains (${e}/${r})`,context:{bondId:t.id}}),(t.a1.biotype!==w||t.a2.biotype!==w)&&i.push({severity:"warning",code:"pair-position-not-base",message:"Hydrogen-bond endpoints are not both bases",context:{bondId:t.id,found:`${t.a1.biotype}/${t.a2.biotype}`}}),Ee(t.a1.symbol,t.a2.symbol)||i.push({severity:"warning",code:"pair-non-canonical",message:`Non-canonical pair ${t.a1.symbol}-${t.a2.symbol}`,context:{bondId:t.id,found:`${t.a1.symbol}-${t.a2.symbol}`}})}for(let[e,t]of o)t>1&&i.push({severity:"warning",code:"pair-already-paired",message:`Base atom ${e} participates in ${t} pair bonds`,context:{atomId:e,found:t}});return i},function(e,t){let i=[];for(let t of e.atoms){let e=t.bio.ambiguity;if(void 0!==e)if("and"===t.bio.ambiguityKind){let n=Be(e,"+");for(let e of n)void 0!==e.ratio&&e.ratio<0&&i.push({severity:"error",code:"ratio-and-negative",message:`AND ratio for '${e.symbol}' is negative (${e.ratio})`,context:{atomId:t.id,found:e.ratio}})}else if("or"===t.bio.ambiguityKind){let n=Be(e,","),o=0,r=!1;for(let e of n)"number"==typeof e.ratio&&(o+=e.ratio,r=!0);r&&Math.abs(o-1)>.001&&Math.abs(o-100)>.5&&i.push({severity:"info",code:"ratio-doesnt-sum-to-1",message:`OR ratios sum to ${o} (expected 1.0 or 100)`,context:{atomId:t.id,found:o}})}}return i},function(e,t){let i=[],n=new Set(e.chains.map(e=>e.id));for(let t of e.annotations.perPolymer.keys())n.has(t)||i.push({severity:"warning",code:"annotation-unknown-polymer",message:`Annotation references unknown polymer '${t}'`,context:{found:t}});return i},function(e,t){let i=[];for(let t of e.chains)t.backboneAtoms.length>1e4&&i.push({severity:"info",code:"polymer-too-long",message:`Polymer '${t.id}' has ${t.backboneAtoms.length} atoms (> 10000); renderer may switch to rows layout`,context:{chainId:t.id,found:t.backboneAtoms.length}});let n=0;for(let t of e.bonds)("cross-polymer"===t.kind||"hbond"===t.kind)&&(n+=1);n>1e3&&i.push({severity:"info",code:"connection-count-high",message:`${n} cross-polymer/hbond connections (> 1000); rendering may be slow`,context:{found:n}});for(let t of e.groups)"bracket"===t.kind&&void 0!==t.repeat&&t.repeat.max>1e4&&i.push({severity:"warning",code:"bracket-repeat-too-large",message:`Bracket repeat upper bound ${t.repeat.max} > 10000`,context:{found:t.repeat.max}});return i}];function Ee(e,t){let i=e.toUpperCase(),n=t.toUpperCase();return new Set(["A:T","T:A","A:U","U:A","G:C","C:G"]).has(`${i}:${n}`)}function Be(e,t){let i=e.trim();i.startsWith("(")&&i.endsWith(")")&&(i=i.slice(1,-1));let n=i.split(t),o=[];for(let e of n){let t=e.trim();if(0===t.length)continue;let i=t.indexOf(":");if(i<0){o.push({symbol:t});continue}let n=t.slice(0,i),r=t.slice(i+1),s=parseFloat(r);Number.isFinite(s)?o.push({symbol:n,ratio:s}):o.push({symbol:n})}return o}function Se(e){let t=new Map;for(let i of e)t.set(i.polymerType,(t.get(i.polymerType)??0)+i.backbone.length);let i=e[0].polymerType,n=-1;for(let o of e){let e=t.get(o.polymerType);e>n&&(i=o.polymerType,n=e)}return i}function Me(e,t,i){let n=(e,t)=>"numeric"===e.kind&&e.r===t,o=[[e.a1,e.r1,e.a2,e.r2],[e.a2,e.r2,e.a1,e.r1]];for(let[e,r,s,a]of o){if(!n(r,2)||!n(a,1))continue;let o=i.get(e.id),l=i.get(s.id);if(void 0===o||void 0===l)continue;let h=t[o],d=t[l];if(h.backbone[h.backbone.length-1].id===e.id&&d.backbone[0].id===s.id)return{tail:o,head:l}}return null}function Te(e,t,i){let n=new Set,o=t;for(;void 0!==o&&!n.has(o);){if(o===i)return!0;n.add(o),o=e.get(o)}return!1}function Ie(e){switch(e){case B.PEPTIDE:return"PEPTIDE";case B.RNA:return"RNA";case B.CHEM:return"CHEM";case B.BLOB:default:return"BLOB"}}function Le(e,t,i,n){if(i.length<2)return!1;let o=i[0],r=i[i.length-1];for(let i of e.bonds){if("backbone"===i.kind||"branch"===i.kind)continue;let e=n.get(i.a1.id),s=n.get(i.a2.id);if(e!==t||s!==t||!(i.a1.id===r.id&&i.a2.id===o.id||i.a2.id===r.id&&i.a1.id===o.id))continue;let 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l=s.monomer?.symbol??s.symbol;if(""!==l){let t=n*(l.length<=1?1:Math.min(1,2/l.length));e.save(),e.fillStyle=a.text,e.font=`${t}px ${i.fontFamily}`,e.textAlign="center",e.textBaseline="middle",e.fillText(l,s.p.x,s.p.y),e.restore()}if(o){let t=.525*r;e.save(),e.fillStyle=i.idColor,e.font=`${.8*n}px ${i.fontFamily}`,e.textAlign="right",e.textBaseline="bottom",e.fillText(String(s.bio.continuousId),s.p.x-t,s.p.y-t),e.restore()}}}(e,t,o,n.fontSize??o.fontSize,n.showIds??!1,n.bondLength??o.bondLength),!1!==n.showAnnotations&&function(e,t,i,n){e.save(),e.fillStyle=i.annotationColor,e.font=`${.7*n}px ${i.fontFamily}`,e.textAlign="left",e.textBaseline="alphabetic";for(let n of t.atoms){let t=n.bio.annotation;if(void 0===t||""===t)continue;let o=Yt(n,i);e.fillText(t,n.p.x+o.size+2,n.p.y-o.size)}e.font=`${.8*n}px ${i.fontFamily}`;for(let n of t.chains){if(void 0===n.annotation||""===n.annotation)continue;let t=n.backboneAtoms[0];void 0!==t&&e.fillText(n.annotation,t.p.x,t.p.y-1.4*i.fontSize)}e.font=`bold ${.85*n}px ${i.fontFamily}`,e.textAlign="center",e.textBaseline="middle";let o=1.4*i.fontSize;for(let i of t.chains){if("RNA"!==i.polymerType)continue;let t=i.backboneAtoms;if(t.length<2)continue;let n=t[0],r=t[t.length-1],s=t.length>=2?t[1]:null,a=t.length>=2?t[t.length-2]:null,l=li(n.p,s?.p??null,o),h=li(r.p,a?.p??null,o),d=void 0!==i.strandType?`5'${i.strandType}`:"5'",c=void 0!==i.strandType?`3'${i.strandType}`:"3'";e.fillText(d,l.x,l.y),e.fillText(c,h.x,h.y)}e.restore()}(e,t,o,n.fontSize??o.fontSize),e.restore(),{bbox:{x:s.x,y:s.y,width:s.width,height:s.height},drawBox:{x:l,y:h,width:a.width,height:a.height}}}function li(e,t,i){if(null===t)return{x:e.x-i,y:e.y};let n=e.x-t.x,o=e.y-t.y,r=Math.hypot(n,o);return 0===r?{x:e.x-i,y:e.y}:{x:e.x+i*(n/r),y:e.y+i*(o/r)}}function hi(e,t,i,n){let o=t.p,r=zt(t.biotype);switch(e.beginPath(),r){case"hexagon":di(e,o,6,i,-30);break;case"diamond":e.moveTo(o.x,o.y-i),e.lineTo(o.x+i,o.y),e.lineTo(o.x,o.y+i),e.lineTo(o.x-i,o.y),e.closePath();break;case"pentagon":di(e,o,5,i,-90);break;case"rounded-rect":case"blob":{let t=i/2,r=Math.max(0,Math.min(n,t)),s=o.x-t,a=o.y-t,l=2*t,h=2*t;e.moveTo(s+r,a),e.lineTo(s+l-r,a),e.quadraticCurveTo(s+l,a,s+l,a+r),e.lineTo(s+l,a+h-r),e.quadraticCurveTo(s+l,a+h,s+l-r,a+h),e.lineTo(s+r,a+h),e.quadraticCurveTo(s,a+h,s,a+h-r),e.lineTo(s,a+r),e.quadraticCurveTo(s,a,s+r,a),e.closePath();break}case"circle":e.ellipse(o.x,o.y,i,i,0,0,2*Math.PI)}}function di(e,t,i,n,o){let r=360/i;for(let s=0;s<i;s++){let i=(o+s*r)*Math.PI/180,a=t.x+n*Math.cos(i),l=t.y+n*Math.sin(i);0===s?e.moveTo(a,l):e.lineTo(a,l)}e.closePath()}function ci(e,t){switch(e.kind){case"backbone":case"branch":case"group":return t.defaultStroke;case"cross-polymer":return t.crossPolymerBondColor;case"hbond":return function(e){if(e.a1.biotype!==w||e.a2.biotype!==w)return!1;let t=mi(e.a1),i=mi(e.a2);for(let[e,n]of pi)if(t===e&&i===n||t===n&&i===e)return!0;return!1}(e)?t.hbondColor:t.nonCanonicalHbondColor}}function ui(e){return 1.125}var pi=[["A","T"],["A","U"],["G","C"]];function mi(e){let t=e.monomer?.naturalAnalog,i=void 0!==t&&""!==t?t:e.symbol;return 0===i.length?"":i.charAt(0).toUpperCase()}function fi(e){let t=new Map,i=new Map;for(let t of e.bonds){let e=t.a1.id,n=t.a2.id,o=i.get(e);void 0===o&&(o=[],i.set(e,o)),o.push(t);let r=i.get(n);void 0===r&&(r=[],i.set(n,r)),r.push(t)}for(let n of e.atoms)Ai(t,n,i.get(n.id)??[]);for(let n of e.groups){if("bracket"!==n.kind)continue;let o=n.repeat?.min??1;if(1===o)continue;let r=new Set(n.members.map(e=>e.target)),s=new Map;for(let t of e.atoms){if(!r.has(t.bio.chainId))continue;let e=new Map;Ai(e,t,i.get(t.id)??[]);for(let[t,i]of e)s.set(t,(s.get(t)??0)+i*(o-1))}for(let[e,i]of s)t.set(e,(t.get(e)??0)+i)}for(let[e,i]of[...t])0===i&&t.delete(e);let n=function(e){let t=0;for(let[i,n]of e){let e=bi[i];void 0!==e&&(t+=e*n)}return Math.round(1e3*t)/1e3}(t);return{elements:t,mw:n}}var bi={H:1.008,C:12.011,N:14.007,O:15.999,F:18.998,Na:22.99,Mg:24.305,P:30.974,S:32.06,Cl:35.45,K:39.098,Ca:40.078,Br:79.904,I:126.904,Fe:55.845,Zn:65.38,Cu:63.546},gi={C:4,N:3,O:2,S:2,P:3,F:1,Cl:1,Br:1,I:1,H:1};function Ai(e,t,i){if(null===t.monomer)return;let n=function(e){let t=vi.get(e);if(void 0!==t)return t;let i=function(e){let t=new Map;if(void 0===e.molfile||""===e.molfile)return{elements:t};let i=function(e){let t=e.split(/\r\n|\n|\r/);if(t.length<5)return null;let i=t[3];if(void 0===i||i.length<6)return null;let n=parseInt(i.slice(0,3),10),o=parseInt(i.slice(3,6),10);if(!Number.isFinite(n)||!Number.isFinite(o)||t.length<4+n+o)return null;let r=[];for(let e=0;e<n;e++){let i=t[4+e];if(void 0===i)return null;let n=i.slice(31,34).trim();r.push(n)}let s=new Array(n).fill(0);for(let e=0;e<o;e++){let i=t[4+n+e];if(void 0===i)return null;let o=parseInt(i.slice(0,3),10),r=parseInt(i.slice(3,6),10),a=parseInt(i.slice(6,9),10);if(!Number.isFinite(o)||!Number.isFinite(r)||!Number.isFinite(a))continue;let l=4===a?1:a;o>=1&&o<=n&&(s[o-1]=(s[o-1]??0)+l),r>=1&&r<=n&&(s[r-1]=(s[r-1]??0)+l)}return{atoms:r,bondOrders:s}}(e.molfile);if(null===i)return{elements:t};let{atoms:n,bondOrders:o}=i;for(let e=0;e<n.length;e++){let i=n[e];if("R"===i||"R#"===i||"*"===i)continue;t.set(i,(t.get(i)??0)+1);let r=gi[i];if(void 0===r)continue;let s=r-(o[e]??0);s>0&&t.set("H",(t.get("H")??0)+s)}for(let i of e.rgroups){let e=i.capGroupName;if(void 0===e)continue;let n=yi(e);for(let[e,i]of n)t.set(e,(t.get(e)??0)+i)}return{elements:t}}(e);return vi.set(e,i),i}(t.monomer);for(let[t,i]of n.elements)e.set(t,(e.get(t)??0)+i);for(let n of i){if("hbond"===n.kind||"group"===n.kind)continue;let i=n.a1.id===t.id?n.r1:n.r2,o=_i(t.monomer,i);if(void 0===o)continue;let r=yi(o);for(let[t,i]of r)e.set(t,(e.get(t)??0)-i)}}function _i(e,t){if("numeric"!==t.kind&&"positional"!==t.kind)return;let i=(t.kind,t.r);for(let t of e.rgroups){let e=/^R([1-9][0-9]*)$/.exec(t.label);if(null!==e&&parseInt(e[1],10)===i)return t.capGroupName}}function yi(e){let t=new Map;switch(e){case"H":t.set("H",1);break;case"OH":t.set("H",1),t.set("O",1)}return t}var vi=new WeakMap;function wi(e){return fi(e).mw}var xi={AA:13.65,AC:10.67,AG:12.79,AU:12.14,CA:10.67,CC:7.52,CG:9.39,CU:8.37,GA:12.79,GC:9.39,GG:11.77,GU:10.21,UA:12.14,UC:8.37,UG:10.21,UU:8.99},Ci={A:15.4,C:7.4,G:11.7,U:10,T:8.8};function ki(e){let t=0;for(let i of e.chains)"PEPTIDE"===i.polymerType?t+=Ei(i.backboneAtoms):"RNA"===i.polymerType&&(t+=Bi(i.backboneAtoms));return Math.round(1e4*t)/1e4}function Ei(e){let t=0,i=0,n=0;for(let o of e){let e=Si(o);"W"===e?t++:"Y"===e?i++:"C"===e&&n++}return 5.5*t+1.49*i+.0625*n}function Bi(e){let t=[];for(let i of e)if(void 0!==i.branchAtom&&i.branchAtom.biotype===w){let e=Si(i.branchAtom);"T"===e&&(e="U"),""!==e&&t.push(e)}if(0===t.length)return 0;if(1===t.length){let e=t[0];return Ci[e]??0}let i=0;for(let e=0;e<t.length-1;e++){let n=t[e],o=t[e+1],r=xi[n+o];void 0!==r&&(i+=r)}let n=0;for(let e=1;e<t.length-1;e++){let i=t[e];n+=Ci[i]??0}return 2*i-n}function Si(e){let t=e.monomer;return null!==t&&void 0!==t.naturalAnalog&&""!==t.naturalAnalog?t.naturalAnalog.charAt(0).toUpperCase():""===e.symbol?"":e.symbol.charAt(0).toUpperCase()}function Mi(e){let t=[];t.push("HWE pseudo-molfile"),t.push(" HWE 2D"),t.push("");let i=e.atoms.length,n=e.bonds.length;t.push(function(e,t){return Li(e)+Li(t)+" 0 0 0 0 0 0 0 0999 V2000"}(i,n));for(let i of e.atoms)t.push(Ti(i));let o=new Map;for(let t=0;t<e.atoms.length;t++)o.set(e.atoms[t].id,t+1);for(let i of e.bonds){let e=o.get(i.a1.id),n=o.get(i.a2.id);void 0===e||void 0===n||t.push(Ii(e,n))}return t.push("M END"),t.join("\n")+"\n"}function Ti(e){let t=function(e){let t=e.monomer;return null!==t&&""!==t.symbol?t.symbol:""!==e.symbol?e.symbol:null!==t&&void 0!==t.naturalAnalog&&""!==t.naturalAnalog?t.naturalAnalog:"X"}(e);return $i(e.p.x)+$i(e.p.y)+$i(0)+" "+function(e){return e.length>=3?e:e+" ".repeat(3-e.length)}(t)+" 0 0 0 0 0 0 0 0 0 0 0 0"}function Ii(e,t){return Li(e)+Li(t)+Li(1)+Li(0)}function Li(e){let t=String(e);return t.length>=3?t:" ".repeat(3-t.length)+t}function $i(e){let t=e.toFixed(4);return t.length>=10?t.slice(0,10):" ".repeat(10-t.length)+t}var Pi=new Map,Ri=class{constructor(e){if(this._destroyed=!1,this._parseHits=0,this._parseMisses=0,this._layoutHits=0,this._layoutMisses=0,this._renderHits=0,this._renderMisses=0,void 0===e.monomerLib||null===e.monomerLib)throw new TypeError("HelmService: options.monomerLib is required");this.monomerLib=e.monomerLib,this.theme=e.theme??Dt,this.logger=e.logger??new h,this.options=Object.freeze({...e});let t=e.cacheSize??256;this._parseCache=new l({max:t}),this._layoutCache=new l({max:t}),this._renderCache=new l({max:t}),this._libUnsub=this.monomerLib.onChanged.subscribe(()=>{this.clearCaches()})}parse(e,t){this._ensureLive(),e=this._normalizeHelm(e);let i=t?.mode??"lenient",n=!1!==t?.resolveMonomers,o=`${(s={mode:i,resolveMonomers:n,helm:e}).mode}|${s.resolveMonomers?1:0}|${s.helm}`,r=this._parseCache.get(o);var s;if(void 0!==r)return this._parseHits+=1,r;this._parseMisses+=1;let a={mode:i,resolveMonomers:n},l=le(e,this.monomerLib,a),h={mol:l.mol,diagnostics:Object.freeze([...l.diagnostics])};return this._parseCache.set(o,h),h}serialize(e,t){return this._ensureLive(),pe(e,{...void 0!==t?.canonicalize?{canonicalize:t.canonicalize}:{},...void 0!==t?.includeHighlights?{includeHighlights:t.includeHighlights}:{},...void 0!==t?.version?{version:t.version}:{}})}validate(e,t){this._ensureLive(),e=this._normalizeHelm(e);let{mol:i,diagnostics:n}=this.parse(e,{mode:"lenient"}),o=void 0!==t?.mode?{mode:t.mode}:{},r=function(e,t,i){let n=i?.mode??"lenient",o=[];for(let i of ke)o.push(...i(e,t));let r="pedantic"===n?o.map(e=>"warning"===e.severity?{...e,severity:"error"}:e):o;if("strict"===n||"pedantic"===n){let e=r.filter(e=>"error"===e.severity);if(e.length>0)throw new s(e)}return r}(i,this.monomerLib,o);return[...n,...r]}canonicalize(e){this._ensureLive(),e=this._normalizeHelm(e);let{mol:t}=this.parse(e,{mode:"lenient"});return pe(new Ae(t).run(),{canonicalize:!0,version:"V2.0"})}removeGaps(e){return this._ensureLive(),function(e,t){let i=function(e){let t=new Map;for(let i of e.atoms)t.set(i.bio.continuousId,i.id);let i=new Set;for(let t of e.atoms)"*"===t.symbol&&i.add(t.id);if(0===i.size)return{mol:e,survivorByOldContinuousId:t};let n=new Map;for(let t of e.atoms)n.set(t.id,[]);for(let t of e.bonds)n.get(t.a1.id)?.push(t),t.a2.id!==t.a1.id&&n.get(t.a2.id)?.push(t);let o=function(e,t){let i=[],n=new Set;for(let o of e){if(n.has(o))continue;let r=new Set,s=[o];for(;s.length>0;){let i=s.pop();if(!r.has(i)){r.add(i),n.add(i);for(let n of t.get(i)??[]){let t=n.a1.id===i?n.a2.id:n.a1.id;e.has(t)&&!r.has(t)&&s.push(t)}}}let a=[],l=new Set;for(let e of r)for(let i of t.get(e)??[])l.has(i.id)||r.has(i.a1.id)!==r.has(i.a2.id)&&(l.add(i.id),a.push(i));i.push({atoms:r,boundary:a})}return i}(i,n);for(let e of o)we(e,n);let r=e.atoms.filter(e=>!i.has(e.id)),s=e.chains.map(e=>({chain:e,backbone:e.backboneAtoms.filter(e=>!i.has(e.id))})).filter(e=>e.backbone.length>0||0===e.chain.backboneAtoms.length),a=new Map,l=new Map;for(let e of s)e.backbone.forEach((t,i)=>{a.set(t.id,e.chain.id),l.set(t.id,i+1)});let h=1;for(let t of e.bonds)t.id>=h&&(h=t.id+1);let d=new Map;for(let e of o){if(2!==e.boundary.length)continue;let t=xe(e,e.boundary[0]),i=xe(e,e.boundary[1]);Ce(t.r,1)&&Ce(i.r,2)&&([t,i]=[i,t]);let n=a.get(t.atom.id)===a.get(i.atom.id),o=l.get(t.atom.id),r=l.get(i.atom.id),s=n&&void 0!==o&&void 0!==r&&o+1===r&&Ce(t.r,2)&&Ce(i.r,1)?"backbone":"cross-polymer",c=Math.min(...e.boundary.map(e=>e.id));d.set(c,{id:h++,a1:t.atom,a2:i.atom,kind:s,r1:t.r,r2:i.r})}let c=[];for(let t of e.bonds){let e=d.get(t.id);void 0!==e&&c.push(e),!i.has(t.a1.id)&&!i.has(t.a2.id)&&c.push(t)}let u=s.map(e=>({id:e.chain.id,polymerType:e.chain.polymerType,backboneAtoms:e.backbone,bonds:c.filter(t=>a.get(t.a1.id)===e.chain.id&&a.get(t.a2.id)===e.chain.id),...void 0!==e.chain.annotation?{annotation:e.chain.annotation}:{}})),p=new Map;for(let e of u){let t=0;for(let i of e.backboneAtoms)t+=1,p.set(i.id,{...i,bio:{...i.bio,positionInChain:t}})}for(let e of r)p.has(e.id)||p.set(e.id,e);for(let[e,t]of p)if(void 0!==t.branchAtom&&i.has(t.branchAtom.id)){let{branchAtom:i,...n}=t;p.set(e,n)}let m=u.map(e=>{let t=e.backboneAtoms.map(e=>p.get(e.id)),i=e.bonds.map(e=>({...e,a1:p.get(e.a1.id),a2:p.get(e.a2.id)}));return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:i,...void 0!==e.annotation?{annotation:e.annotation}:{}}}),f=c.map(e=>({...e,a1:p.get(e.a1.id),a2:p.get(e.a2.id)}));return{mol:{atoms:r.map(e=>p.get(e.id)),bonds:f,chains:m,groups:e.groups,annotations:e.annotations},survivorByOldContinuousId:t}}(le(e,t??null,{mode:"lenient",resolveMonomers:!1}).mol),n=function(e){let t=M(e),i=new Map;for(let n of e.atoms){let e=t.get(n.id);void 0!==e&&e!==n.bio.continuousId?i.set(n.id,{...n,bio:{...n.bio,continuousId:e}}):i.set(n.id,n)}for(let t of e.atoms){if(void 0===t.branchAtom)continue;let e=i.get(t.id),n=i.get(t.branchAtom.id);void 0===e||void 0===n||(e.branchAtom=n)}let n=e.bonds.map(e=>{let t=i.get(e.a1.id),n=i.get(e.a2.id);return void 0===t||void 0===n||t===e.a1&&n===e.a2?e:{...e,a1:t,a2:n}}),o=new Map;for(let e of n)o.set(e.id,e);let r=e.chains.map(e=>{let t=[];for(let n of e.backboneAtoms){let e=i.get(n.id);t.push(e??n)}let n=[];for(let t of e.bonds){let e=o.get(t.id);n.push(e??t)}return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:n,...void 0!==e.annotation?{annotation:e.annotation}:{}}});return{atoms:e.atoms.map(e=>i.get(e.id)??e),bonds:n,chains:r,groups:e.groups,annotations:e.annotations}}(i.mol),o=new Map;for(let e of n.atoms)o.set(e.id,e.bio.continuousId);let r=new Map;for(let[e,t]of i.survivorByOldContinuousId){let i=o.get(t);void 0!==i&&r.set(e,i)}return{srcHelm:e,resHelm:pe(n,{version:"V2.0"}),monomerMap:r}}(this._normalizeHelm(e),this.monomerLib)}renderToSvg(e,t){this._ensureLive(),e=this._normalizeHelm(e);let i=this._resolveRenderOptions(t),n=this._renderKey(e,i),o=this._renderCache.get(n);if(void 0!==o)return this._renderHits+=1,o;this._renderMisses+=1;let{mol:r}=this.parse(e,{mode:"lenient"}),s=this._layout(r,i.bondLength),{svg:a}=Jt(s,i);return this._renderCache.set(n,a),a}renderMol(e,t){this._ensureLive();let i=this._resolveRenderOptions(t),{svg:n}=Jt(e,i);return n}renderMolResult(e,t){return this._ensureLive(),Jt(e,this._resolveRenderOptions(t))}async renderToPng(e,t){if(this._ensureLive(),e=this._normalizeHelm(e),"function"!=typeof globalThis.OffscreenCanvas)throw new a("png-rendering-requires-browser","HelmService.renderToPng requires OffscreenCanvas (browser-only).");let i=this._resolveRenderOptions(t),{mol:n}=this.parse(e,{mode:"lenient"});return async function(e,t={}){let i=function(){let e=globalThis;return"function"==typeof e.OffscreenCanvas?e.OffscreenCanvas:null}();if(null===i&&void 0===t.canvas)throw new Error("renderToPng: OffscreenCanvas is not available in this environment");let n=t.theme??Dt,o=t.width??400,r=t.height??100,s=t.pixelRatio??1,a=t.canvas??new i(Math.max(1,Math.round(o*s)),Math.max(1,Math.round(r*s))),l=a.getContext("2d");if(null===l)throw new Error("renderToPng: failed to acquire 2D context");l.save(),l.scale(s,s),ai(l,e,{x:0,y:0,width:o,height:r},{...t,backColor:t.backColor??n.background}),l.restore();let h=a;if("function"!=typeof h.convertToBlob)throw new Error("renderToPng: canvas.convertToBlob is not available");let d=await(await h.convertToBlob({type:"image/png"})).arrayBuffer();return new Uint8Array(d)}(this._layout(n,i.bondLength),i)}renderToCanvas(e,t,i,n){this._ensureLive(),t=this._normalizeHelm(t);let o=this._resolveRenderOptions(n),{mol:r}=this.parse(t,{mode:"lenient"}),s=this._layout(r,o.bondLength),{bbox:a,drawBox:l}=ai(e,s,i,o);return{mol:s,bbox:a,drawBox:l}}renderMolToCanvas(e,t,i,n){this._ensureLive();let o=this._resolveRenderOptions(n),{bbox:r,drawBox:s}=ai(e,t,i,o);return{mol:t,bbox:r,drawBox:s}}*renderMany(e,t){for(let i of e??[]){let e=this.renderToSvg(i.helm,t);yield{id:i.id,svg:e}}}getFormula(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:"lenient"});return fi(t)}getMolWeight(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:"lenient"});return wi(t)}getExtinctionCoefficient(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:"lenient"});return ki(t)}getMolfile(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:"lenient"});return Mi(t)}hasAtomicMolfileProvider(){return"function"==typeof this.options.atomicMolfileProvider}async getAtomicMolfile(e){this._ensureLive(),e=this._normalizeHelm(e);let t=this.options.atomicMolfileProvider;if("function"!=typeof t)throw new a("atomic-molfile-not-configured","Set HelmServiceOptions.atomicMolfileProvider to enable atomic-level expansion.");return await t(e,this.monomerLib)}hasExtraPanes(){let e=this.options.extraPanes;return void 0!==e&&e.size>0}getExtraPanes(){return this.options.extraPanes??Pi}invalidate(e){if(void 0!==e)for(let t of[this._parseCache,this._layoutCache,this._renderCache]){let i=[];for(let n of t.keys())e(n)&&i.push(n);for(let e of i)t.delete(e)}else this.clearCaches()}clearCaches(){this._parseCache.clear(),this._layoutCache.clear(),this._renderCache.clear(),this._parseHits=0,this._parseMisses=0,this._layoutHits=0,this._layoutMisses=0,this._renderHits=0,this._renderMisses=0}destroy(){this._destroyed||(this._destroyed=!0,this._libUnsub(),this.clearCaches())}_ensureLive(){if(this._destroyed)throw new a("service-destroyed","HelmService instance has been destroyed.")}_normalizeHelm(e){return null==e?"":"string"==typeof e?e:String(e)}_resolveRenderOptions(e){let t={},i=e?.theme??this.theme;return t.theme=i,void 0!==e?.width&&(t.width=e.width),void 0!==e?.height&&(t.height=e.height),void 0!==e?.backColor&&(t.backColor=e.backColor),void 0!==e?.padding&&(t.padding=e.padding),void 0!==e?.showIds&&(t.showIds=e.showIds),void 0!==e?.showAnnotations&&(t.showAnnotations=e.showAnnotations),void 0!==e?.bondLength&&(t.bondLength=e.bondLength),void 0!==e?.fontSize&&(t.fontSize=e.fontSize),void 0!==e?.maxScale&&(t.maxScale=e.maxScale),void 0!==e?.showRGroupLabels&&(t.showRGroupLabels=e.showRGroupLabels),void 0!==e?.selectedAtomIds&&(t.selectedAtomIds=e.selectedAtomIds),void 0!==e?.highlightedAtomIds&&(t.highlightedAtomIds=e.highlightedAtomIds),void 0!==e?.fixedModelBbox&&(t.fixedModelBbox=e.fixedModelBbox),t}_renderKey(e,t){let i=(t.theme??this.theme).name;return`${this._libCacheTag()}|${i}|${t.width??0}x${t.height??0}|p${t.padding??-1}|b${t.bondLength??-1}|bg${t.backColor??""}|i${!0===t.showIds?1:0}a${!1===t.showAnnotations?0:1}|s${t.maxScale??1}|w${xt()}|${e}`}_layout(e,t){let i=`${(r=e).chains.map(e=>`${e.id}:${e.polymerType}:${e.backboneAtoms.length}`).join(",")}#${r.atoms.map(e=>`${e.id}@${e.symbol}@${e.bio.chainId}`).join(";")}#${r.bonds.map(e=>`${e.id}:${e.a1.id}-${e.a2.id}:${e.kind}`).join(";")}`,n=`${this._libCacheTag()}|${t??"d"}|w${xt()}|${i}`,o=this._layoutCache.get(n);var r;if(void 0!==o)return this._layoutHits+=1,o;this._layoutMisses+=1;let s=void 0!==t?Et(e,{bondLength:t}):Et(e);return this._layoutCache.set(n,s),s}get stats(){return{parseHits:this._parseHits,parseMisses:this._parseMisses,layoutHits:this._layoutHits,layoutMisses:this._layoutMisses,renderHits:this._renderHits,renderMisses:this._renderMisses}}_libCacheTag(){let e=this.monomerLib,t="number"==typeof e.version?e.version:0;return`${this.monomerLib.source}@${t}`}},Hi=class{constructor(e,t){this.atoms=e,this.bonds=t,this.isEmpty=0===e.size&&0===t.size,Object.freeze(this)}},Ni=new Hi(new Set,new Set),Di={empty:()=>Ni,fromAtoms:e=>new Hi(new Set(e),new Set),fromBonds:e=>new Hi(new Set,new Set(e)),fromAtomsAndBonds:(e,t)=>new Hi(new Set(e),new Set(t)),union(...e){if(0===e.length)return Ni;let t=new Set,i=new Set;for(let n of e){for(let e of n.atoms)t.add(e);for(let e of n.bonds)i.add(e)}return new Hi(t,i)},difference(e,t){let i=new Set,n=new Set;for(let n of e.atoms)t.atoms.has(n)||i.add(n);for(let i of e.bonds)t.bonds.has(i)||n.add(i);return new Hi(i,n)},intersect(e,t){let i=new Set,n=new Set;for(let n of e.atoms)t.atoms.has(n)&&i.add(n);for(let i of e.bonds)t.bonds.has(i)&&n.add(i);return new Hi(i,n)},toggle(e,t){if("atom"===t.kind){let i=new Set(e.atoms);return i.has(t.id)?i.delete(t.id):i.add(t.id),new Hi(i,new Set(e.bonds))}let i=new Set(e.bonds);return i.has(t.id)?i.delete(t.id):i.add(t.id),new Hi(new Set(e.atoms),i)},hasAtom:(e,t)=>e.atoms.has(t),hasBond:(e,t)=>e.bonds.has(t),equals(e,t){if(e===t)return!0;if(e.atoms.size!==t.atoms.size||e.bonds.size!==t.bonds.size)return!1;for(let i of e.atoms)if(!t.atoms.has(i))return!1;for(let i of e.bonds)if(!t.bonds.has(i))return!1;return!0}};function Fi(e){let t=e.monomer;return null===t?0:t.rgroups.length}function Oi(e,t){let i=Fi(e);if(0===i)return[];let n=new Set(function(e,t){let i=new Set;for(let n of t)n.a1.id===e.id&&"numeric"===n.r1.kind&&i.add(n.r1.r),n.a2.id===e.id&&"numeric"===n.r2.kind&&i.add(n.r2.r);let n=[],o=Array.from(i).sort((e,t)=>e-t);for(let e of o)n.push(e);return n}(e,t)),o=[];for(let e=1;e<=i;e++)n.has(e)||o.push(e);return o}function zi(e,t){let i=[];for(let n of t)if(n.a1.id===e.id){let e="numeric"===n.r1.kind?n.r1.r:0;i.push({bond:n,side:"r1",rNumber:e})}else if(n.a2.id===e.id){let e="numeric"===n.r2.kind?n.r2.r:0;i.push({bond:n,side:"r2",rNumber:e})}return i}function Gi(e,t){return e.kind===t.kind&&("numeric"===e.kind&&"numeric"===t.kind?e.r===t.r:"positional"!==e.kind||"positional"!==t.kind||e.position===t.position&&e.r===t.r)}var qi=class{constructor(e){this._atoms=new Map,this._atomOrder=[],this._bonds=new Map,this._bondOrder=[],this._chains=new Map,this._chainOrder=[],this._addedAtoms=new Set,this._removedAtoms=new Set,this._modifiedAtoms=new Set,this._addedBonds=new Set,this._removedBonds=new Set,this._modifiedBonds=new Set,this._topologyDirty=!1,this._idgen=new S;let t=function(e){let t=0;for(let i of e.atoms)i.id>t&&(t=i.id);for(let i of e.bonds)i.id>t&&(t=i.id);return t}(e);for(let e=0;e<t;e++)this._idgen.next();for(let t of e.chains)this._chains.set(t.id,{id:t.id,polymerType:t.polymerType,backboneAtomIds:t.backboneAtoms.map(e=>e.id),bondIds:t.bonds.map(e=>e.id),annotation:t.annotation}),this._chainOrder.push(t.id);for(let t of e.atoms)this._atoms.set(t.id,{id:t.id,p:{x:t.p.x,y:t.p.y},biotype:t.biotype,symbol:t.symbol,monomer:t.monomer,bio:{...t.bio},hidden:t.hidden,selected:t.selected,highlighted:t.highlighted,tag:t.tag,branchAtomId:t.branchAtom?.id,inlineSource:t.inlineSource}),this._atomOrder.push(t.id);for(let t of e.bonds)this._bonds.set(t.id,{id:t.id,a1Id:t.a1.id,a2Id:t.a2.id,kind:t.kind,r1:t.r1,r2:t.r2,ratio:t.ratio,tag:t.tag}),this._bondOrder.push(t.id);this._groups=[...e.groups],this._annotations=e.annotations}addAtom(e){let t=this._idgen.next(),i=function(e){switch(e){case y:return B.PEPTIDE;case v:case w:case x:case E:return B.RNA;case C:return B.CHEM;case k:return B.BLOB}}(e.biotype),n=e.chainId??this._pickChainId(i),o=this._chains.get(n);void 0===o&&(o={id:n,polymerType:i,backboneAtomIds:[],bondIds:[],annotation:void 0},this._chains.set(n,o),this._chainOrder.push(n));let r=e.positionInChain??o.backboneAtomIds.length+1,s={id:t,p:{x:e.p.x,y:e.p.y},biotype:e.biotype,symbol:e.symbol,monomer:null,bio:{chainId:n,positionInChain:r,continuousId:0},hidden:!1,selected:!1,highlighted:!1,tag:void 0,branchAtomId:void 0,inlineSource:void 0};this._atoms.set(t,s),this._atomOrder.push(t);let a=Math.max(0,Math.min(r-1,o.backboneAtomIds.length));return o.backboneAtomIds.splice(a,0,t),this._addedAtoms.add(t),this._topologyDirty=!0,t}removeAtom(e){let t=this._atoms.get(e);if(void 0===t)return;let i=[];for(let t of this._bonds.values())(t.a1Id===e||t.a2Id===e)&&i.push(t.id);for(let e of i)this._removeBondInternal(e);for(let t of this._atoms.values())t.branchAtomId===e&&(t.branchAtomId=void 0);let n=this._chains.get(t.bio.chainId);if(void 0!==n){let t=n.backboneAtomIds.indexOf(e);t>=0&&n.backboneAtomIds.splice(t,1)}this._atoms.delete(e);let o=this._atomOrder.indexOf(e);o>=0&&this._atomOrder.splice(o,1),this._addedAtoms.has(e)?this._addedAtoms.delete(e):this._removedAtoms.add(e),this._modifiedAtoms.delete(e),this._topologyDirty=!0}updateAtom(e,t){let i=this._atoms.get(e);void 0!==i&&(void 0!==t.p&&(i.p={x:t.p.x,y:t.p.y}),void 0!==t.symbol&&(i.symbol=t.symbol),void 0!==t.selected&&(i.selected=t.selected),void 0!==t.highlighted&&(i.highlighted=t.highlighted),"tag"in t&&(i.tag=t.tag),void 0!==t.hidden&&(i.hidden=t.hidden),this._addedAtoms.has(e)||this._modifiedAtoms.add(e))}addBond(e){if(!this._atoms.has(e.a1))throw new Error(`Transaction.addBond: atom ${e.a1} does not exist`);if(!this._atoms.has(e.a2))throw new Error(`Transaction.addBond: atom ${e.a2} does not exist`);for(let t of this._bonds.values()){let i=t.a1Id===e.a1&&t.a2Id===e.a2&&Gi(t.r1,e.r1)&&Gi(t.r2,e.r2),n=t.a1Id===e.a2&&t.a2Id===e.a1&&Gi(t.r1,e.r2)&&Gi(t.r2,e.r1);if(i||n)throw new Error(`Transaction.addBond: duplicate bond ${e.a1}:${ji(e.r1)}-${e.a2}:${ji(e.r2)}`)}let t=this._idgen.next();this._bonds.set(t,{id:t,a1Id:e.a1,a2Id:e.a2,kind:e.kind,r1:e.r1,r2:e.r2,ratio:void 0,tag:void 0}),this._bondOrder.push(t);let i=this._atoms.get(e.a1),n=this._atoms.get(e.a2);if(void 0!==i&&void 0!==n&&i.bio.chainId===n.bio.chainId){let e=this._chains.get(i.bio.chainId);void 0!==e&&e.bondIds.push(t)}return this._addedBonds.add(t),this._topologyDirty=!0,t}removeBond(e){this._bonds.has(e)&&(this._removeBondInternal(e),this._topologyDirty=!0)}updateBond(e,t){let i=this._bonds.get(e);void 0!==i&&("tag"in t&&(i.tag=t.tag),"ratio"in t&&(i.ratio=t.ratio),this._addedBonds.has(e)||this._modifiedBonds.add(e))}commit(){let e=new Map;for(let t of this._atomOrder){let i=this._atoms.get(t);if(void 0===i)continue;let n={id:i.id,p:{x:i.p.x,y:i.p.y},biotype:i.biotype,symbol:i.symbol,monomer:i.monomer,bio:{...i.bio},hidden:i.hidden,selected:i.selected,highlighted:i.highlighted,...void 0!==i.tag?{tag:i.tag}:{},...void 0!==i.inlineSource?{inlineSource:i.inlineSource}:{}};e.set(t,n)}for(let t of this._atomOrder){let i=this._atoms.get(t);if(void 0===i||void 0===i.branchAtomId)continue;let n=e.get(t),o=e.get(i.branchAtomId);void 0===n||void 0===o||(n.branchAtom=o)}let t=new Map;for(let i of this._bondOrder){let n=this._bonds.get(i);if(void 0===n)continue;let o=e.get(n.a1Id),r=e.get(n.a2Id);if(void 0===o||void 0===r)continue;let s={id:n.id,a1:o,a2:r,kind:n.kind,r1:n.r1,r2:n.r2,...void 0!==n.ratio?{ratio:{...n.ratio}}:{},...void 0!==n.tag?{tag:n.tag}:{}};t.set(i,s)}let i=[];for(let n of this._chainOrder){let o=this._chains.get(n);if(void 0===o||0===o.backboneAtomIds.length&&0===o.bondIds.length)continue;let r=[];for(let t of o.backboneAtomIds){let i=e.get(t);void 0!==i&&r.push(i)}let s=[];for(let e of o.bondIds){let i=t.get(e);void 0!==i&&s.push(i)}i.push({id:o.id,polymerType:o.polymerType,backboneAtoms:r,bonds:s,...void 0!==o.annotation?{annotation:o.annotation}:{}})}let n={atoms:this._atomOrder.map(t=>e.get(t)).filter(e=>void 0!==e),bonds:this._bondOrder.map(e=>t.get(e)).filter(e=>void 0!==e),chains:i,groups:[...this._groups],annotations:this._annotations};this._topologyDirty&&(n=function(e){let t=M(e),i=new Map;for(let n of e.atoms){let e=t.get(n.id);void 0!==e&&e!==n.bio.continuousId?i.set(n.id,{...n,bio:{...n.bio,continuousId:e}}):i.set(n.id,n)}for(let t of e.atoms){if(void 0===t.branchAtom)continue;let e=i.get(t.id),n=i.get(t.branchAtom.id);void 0===e||void 0===n||(e.branchAtom=n)}let n=e.bonds.map(e=>{let t=i.get(e.a1.id),n=i.get(e.a2.id);return void 0===t||void 0===n||t===e.a1&&n===e.a2?e:{...e,a1:t,a2:n}}),o=new Map;for(let e of n)o.set(e.id,e);let r=e.chains.map(e=>{let t=[];for(let n of e.backboneAtoms)t.push(i.get(n.id)??n);let n=[];for(let t of e.bonds)n.push(o.get(t.id)??t);return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:n,...void 0!==e.annotation?{annotation:e.annotation}:{}}});return{atoms:e.atoms.map(e=>i.get(e.id)??e),bonds:n,chains:r,groups:e.groups,annotations:e.annotations}}(n));let o=Object.freeze({addedAtomIds:new Set(this._addedAtoms),removedAtomIds:new Set(this._removedAtoms),addedBondIds:new Set(this._addedBonds),removedBondIds:new Set(this._removedBonds),modifiedAtomIds:new Set(this._modifiedAtoms),modifiedBondIds:new Set(this._modifiedBonds)});return this._addedAtoms.clear(),this._removedAtoms.clear(),this._modifiedAtoms.clear(),this._addedBonds.clear(),this._removedBonds.clear(),this._modifiedBonds.clear(),this._topologyDirty=!1,{mol:n,changes:o}}_removeBondInternal(e){if(void 0===this._bonds.get(e))return;this._bonds.delete(e);let t=this._bondOrder.indexOf(e);t>=0&&this._bondOrder.splice(t,1);for(let t of this._chains.values()){let i=t.bondIds.indexOf(e);i>=0&&t.bondIds.splice(i,1)}this._addedBonds.has(e)?this._addedBonds.delete(e):this._removedBonds.add(e),this._modifiedBonds.delete(e)}_pickChainId(e){let t=function(e){switch(e){case B.PEPTIDE:return"PEPTIDE";case B.RNA:return"RNA";case B.CHEM:return"CHEM";case B.BLOB:return"BLOB";case B.G:return"G"}}(e),i=1;for(;this._chains.has(`${t}${i}`);)i+=1;return`${t}${i}`}};function ji(e){switch(e.kind){case"numeric":return`R${e.r}`;case"unspecified":return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${e.position}pos:R${e.r}`}}var Yi=class{constructor(e,t,i){this.atoms=[],this.bonds=[],this.bondHitWidth=i?.bondHitWidth??4,this.rebuild(e,t)}rebuild(e,t){let i=[];for(let n of e.atoms)n.hidden||i.push({atom:n,bbox:qt(n,t),hitRadius:jt(n,t)});let n=[];for(let t of e.bonds)n.push({bond:t,a:t.a1.p,b:t.a2.p});this.atoms=i,this.bonds=n}test(e){let t=null,i=null;for(let n of this.atoms){if(!Vi(e,n.bbox))continue;let o=e.x-n.atom.p.x,r=e.y-n.atom.p.y,s=Math.sqrt(o*o+r*r);s>n.hitRadius||(null===t||s<t.d?(i=t,t={entry:n,d:s}):(null===i||s<i.d)&&(i={entry:n,d:s}))}if(null!==t)return{atom:t.entry.atom};let n=null;for(let t of this.bonds){let i=Wi(e,t.a,t.b);i>this.bondHitWidth||(null===n||i<n.d)&&(n={entry:t,d:i})}return null!==n?{bond:n.entry.bond}:null}testRect(e){let t=[];for(let i of this.atoms)Vi(i.atom.p,e)&&t.push(i.atom);let i=[];for(let t of this.bonds)Vi(t.a,e)&&Vi(t.b,e)&&i.push(t.bond);return{atoms:t,bonds:i}}atomCount(){return this.atoms.length}bondCount(){return this.bonds.length}};function Vi(e,t){return e.x>=t.x&&e.x<=t.x+t.width&&e.y>=t.y&&e.y<=t.y+t.height}function Wi(e,t,i){let n=i.x-t.x,o=i.y-t.y,r=n*n+o*o;if(0===r){let i=e.x-t.x,n=e.y-t.y;return Math.sqrt(i*i+n*n)}let s=((e.x-t.x)*n+(e.y-t.y)*o)/r;s<0?s=0:s>1&&(s=1);let a=t.x+s*n,l=t.y+s*o,h=e.x-a,d=e.y-l;return Math.sqrt(h*h+d*d)}var Ui=class{constructor(){this._handlers=new Map}on(e,t){let i=this._handlers.get(e);void 0===i&&(i=new Set,this._handlers.set(e,i));let n=t;return i.add(n),()=>{let t=this._handlers.get(e);void 0!==t&&t.delete(n)}}off(e,t){let i=this._handlers.get(e);void 0!==i&&i.delete(t)}fire(e,t){let i=this._handlers.get(e);if(void 0===i||0===i.size)return;let n=[...i];for(let e of n)e(t)}clear(){this._handlers.clear()}observerCount(e){if(void 0===e){let e=0;for(let t of this._handlers.values())e+=t.size;return e}return this._handlers.get(e)?.size??0}},Ki=class{constructor(e){this._entries=[],this._idx=-1;let t=e?.maxEntries??100;if(t<=0)throw new RangeError("HistoryStack: maxEntries must be > 0");this._max=t}push(e){for(this._idx<this._entries.length-1&&(this._entries=this._entries.slice(0,this._idx+1)),this._entries.push(e),this._idx=this._entries.length-1;this._entries.length>this._max;)this._entries.shift(),this._idx-=1}canUndo(){return this._idx>0}canRedo(){return this._idx>=0&&this._idx<this._entries.length-1}undo(){return 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svgRoot(){return this._svgRoot}get width(){return this._width}get height(){return this._height}resize(e,t){this._destroyed||(this._width=e,this._height=t,this._renderFresh())}redraw(){this._destroyed||this._renderFresh()}destroy(){if(this._destroyed)return;this._destroyed=!0;for(let e of this._unsubs)e();this._unsubs.length=0;let e=this.host.querySelector(".hw-editor-view");null!==e&&null!==e.parentNode&&e.parentNode.removeChild(e),nn(this._tooltip),nn(this._bondTooltip),this._tooltip=null,this._bondTooltip=null}_renderFresh(){let e=this._editor.getService(),t=this._currentTheme(),i=this._editor.getMol();null===this._pinnedBbox&&(this._pinnedBbox=ei(i,t));let n=e.renderMol(i,{width:this._width,height:this._height,theme:t,fixedModelBbox:this._pinnedBbox});this._svgRoot=function(e,t){let i=Xi(e),n=e.querySelector(".hw-editor-view");if(null===n)throw new Error("EditorView.replaceSvg: missing .hw-editor-view wrapper.");let o=i.createElement("div");o.innerHTML=t;let 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s=Zi(i,o,220,140);if(this._rdkitSvgCache.size>=e._RDKIT_CACHE_LIMIT){let e=this._rdkitSvgCache.keys().next().value;void 0!==e&&this._rdkitSvgCache.delete(e)}return this._rdkitSvgCache.set(r,s),s}_hideTooltip(){nn(this._tooltip)}_showBondTooltip(e,t,i){let n=this._bondTooltip;if(null===n)return;let o=an(e.r1),r=an(e.r2),s=`${e.a1.symbol}@${e.a1.bio.chainId}:${e.a1.bio.positionInChain}`,a=`${e.a2.symbol}@${e.a2.bio.chainId}:${e.a2.bio.positionInChain}`;en(this._doc,n,{symbol:`${o}-${r} (${e.kind})`,name:`${s} ↔ ${a}`}),tn(n,t,i)}_hideBondTooltip(){nn(this._bondTooltip)}_paintBondPreview(e,t,i){let n=this._svgRoot.querySelector(".hw-content");if(null===n)return;let o=n.querySelector(".hw-bond-preview");null===o&&(o=this._doc.createElementNS("http://www.w3.org/2000/svg","line"),o.setAttribute("class","hw-bond-preview"),o.setAttribute("data-testid","bond-preview"),o.setAttribute("stroke-dasharray","6 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r=o.querySelector(".hw-selection-rect");null===r&&(r=this._doc.createElementNS("http://www.w3.org/2000/svg","rect"),r.setAttribute("class","hw-selection-rect"),r.setAttribute("data-testid","selection-rect"),r.setAttribute("fill","rgba(31, 95, 205, 0.08)"),r.setAttribute("stroke","#1f5fcd"),r.setAttribute("stroke-width","1"),r.setAttribute("stroke-dasharray","4 3"),r.setAttribute("pointer-events","none"),o.appendChild(r)),r.setAttribute("x",String(e)),r.setAttribute("y",String(t)),r.setAttribute("width",String(i)),r.setAttribute("height",String(n))}_clearSelectionRect(){let e=this._svgRoot.querySelector(".hw-selection-rect");null!==e&&null!==e.parentNode&&e.parentNode.removeChild(e)}};rn._RDKIT_CACHE_LIMIT=256;var sn=rn;function an(e){switch(e.kind){case"numeric":return`R${e.r}`;case"unspecified":return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${e.position}pos:R${e.r}`}}var ln=class e{constructor(e,t){this._onClose=null,this._primaryAction=null,this._host=e,this._doc=t.documentImpl??Xi(e);let i=this._doc,n={class:"hw-modal-backdrop",role:"presentation"};void 0!==t.testId&&(n["data-testid"]=`dialog-${t.testId}`);let o=Qi(i,"div",n),r={class:"hw-modal",role:"dialog","aria-modal":"true","aria-label":t.title};void 0!==t.testId&&(r["data-testid"]=`dialog-${t.testId}-frame`);let s=Qi(i,"div",r),a=Qi(i,"div",{class:"hw-modal__header"},[t.title]),l=Qi(i,"div",{class:"hw-modal__body"});s.appendChild(a),s.appendChild(l),o.appendChild(s);let h=e=>{e.stopPropagation()};for(let e of["mousedown","mousemove","mouseup","mouseover","mouseenter","mouseleave","wheel","contextmenu","dblclick","keydown","keyup","keypress"])o.addEventListener(e,h);s.addEventListener("keydown",e=>{let t=e;if("Enter"!==t.key||"TEXTAREA"===t.target?.tagName)return;let 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s.setAttribute("id",o),s.setAttribute("type","text"),s.setAttribute("class","hw-modal__input"),void 0!==n&&s.setAttribute("data-testid",n),s.value=i,{row:Qi(e,"div",{class:"hw-modal__row"},[r,s]),input:s}}function cn(e,t,i,n,o){let r=`hw-sel-${Math.random().toString(36).slice(2,9)}`,s=Qi(e,"label",{for:r,class:"hw-modal__label"},[t]),a=e.createElement("select");a.setAttribute("id",r),a.setAttribute("class","hw-modal__select"),void 0!==o&&a.setAttribute("data-testid",o);for(let t of i){let i=e.createElement("option");i.setAttribute("value",t.value),t.value===n&&i.setAttribute("selected",""),i.appendChild(e.createTextNode(t.label)),a.appendChild(i)}return{row:Qi(e,"div",{class:"hw-modal__row"},[s,a]),select:a}}function un(e,t){let i=e.createElement("button");i.setAttribute("class","hw-modal__ok"),i.setAttribute("type","button"),void 0!==t&&i.setAttribute("data-testid",`${t}-ok`),i.appendChild(e.createTextNode("OK"));let n=e.createElement("button");return n.setAttribute("class","hw-modal__cancel"),n.setAttribute("type","button"),void 0!==t&&n.setAttribute("data-testid",`${t}-cancel`),n.appendChild(e.createTextNode("Cancel")),{row:Qi(e,"div",{class:"hw-modal__actions"},[i,n]),ok:i,cancel:n}}var pn=class{constructor(e,t){this._modal=null,this._editor=e;let i=e._getHost();if(null===i)throw new Error("ChooseRDialog: editor has no host element.");this._doc=t?.documentImpl??Xi(i)}open(e,t,i){this.close();let n=this._editor._getHost();if(null===n)return Promise.resolve(null);let o=new hn(n,{documentImpl:this._doc,title:"Choose R-Groups",testId:"choose-r"});this._modal=o;let r=fn(e,i?.freeR1,i?.currentR1,this._editor),s=fn(t,i?.freeR2,i?.currentR2,this._editor),a=Qi(this._doc,"div",{class:"hw-modal__info"},[`${e.symbol} (${e.bio.chainId})`]),l=void 0!==i?.currentR1?String(i.currentR1):r[0]?.value??"1",h=void 0!==i?.currentR2?String(i.currentR2):s[0]?.value??"1",d=cn(this._doc,"R-group on side 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null!==this._modal&&this._modal.isOpen}close(){null!==this._modal&&(this._modal.close(),this._modal=null)}};function mn(e){let t=e.value;if("string"==typeof t&&t.length>0){let e=Number(t);if(Number.isFinite(e)&&e>=1)return e}let i=e.querySelectorAll("option");for(let e of Array.from(i))if(null!==e.getAttribute("selected")){let t=e.getAttribute("value")??"",i=Number(t);if(Number.isFinite(i)&&i>=1)return i}let n=i[0];if(void 0!==n){let e=n.getAttribute("value")??"",t=Number(e);if(Number.isFinite(t)&&t>=1)return t}return 1}function fn(e,t,i,n){let o,r=e.monomer?.rgroups;if(void 0===r||0===r.length)return[{value:"1",label:"R1"},{value:"2",label:"R2"},{value:"3",label:"R3"}];if(void 0!==t)o=new Set(t);else if(o=new Set(Oi(e,n.getMol().bonds)),0===o.size)for(let e=1;e<=r.length;e++)o.add(e);void 0!==i&&i>=1&&i<=r.length&&o.add(i);let s=[],a=Array.from(o).sort((e,t)=>e-t);for(let e of a){let t=r[e-1];if(void 0===t)continue;let i=void 0!==t.capGroupName&&""!==t.capGroupName?` (${t.capGroupName})`:"";s.push({value:String(e),label:`${t.label}${i}`})}return s}var bn="next-add-cursor";function gn(e){null!==e&&(e.style.display="none")}var An=class{constructor(e,t,i){this._hoverAtom=null,this._hoverBond=null,this._dragOrigin=null,this._bondStart=null,this._bondDragMoved=!1,this._rectDragHappened=!1,this._chooseRDialog=null,this._panStart=null,this._atomDragState=null,this._panMoved=!1,this._atomDragMoved=!1,this._nextAddCursorEl=null,this._destroyed=!1,this._unsubs=[],this._host=e,this._editor=t,this._enableContextMenu=i?.enableContextMenu??!0,this._tester=new Yi(t.getMol(),t._currentTheme()),this._unsubs.push(t.on("mol:changed",()=>{this._tester=new Yi(this._editor.getMol(),this._editor._currentTheme()),this._hoverAtom=null,this._hoverBond=null})),this._unsubs.push(t.on("option:change",e=>{("mode"===e.key||"nextAdd"===e.key)&&gn(this._nextAddCursorEl)})),this._onMove=e=>this._handleMove(e),this._onClick=e=>this._handleClick(e),this._onDblClick=e=>this._handleDblClick(e),this._onContextMenu=e=>this._handleContextMenu(e),this._onMouseDown=e=>this._handleMouseDown(e),this._onMouseUp=e=>this._handleMouseUp(e),this._onMouseLeave=e=>this._handleMouseLeave(e),this._onWheel=e=>this._handleWheel(e),e.addEventListener("mousemove",this._onMove),e.addEventListener("click",this._onClick),e.addEventListener("dblclick",this._onDblClick),e.addEventListener("contextmenu",this._onContextMenu),e.addEventListener("mousedown",this._onMouseDown),e.addEventListener("mouseup",this._onMouseUp),e.addEventListener("mouseleave",this._onMouseLeave),e.addEventListener("wheel",this._onWheel,{passive:!1})}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();this._host.removeEventListener("mousemove",this._onMove),this._host.removeEventListener("click",this._onClick),this._host.removeEventListener("dblclick",this._onDblClick),this._host.removeEventListener("contextmenu",this._onContextMenu),this._host.removeEventListener("mousedown",this._onMouseDown),this._host.removeEventListener("mouseup",this._onMouseUp),this._host.removeEventListener("mouseleave",this._onMouseLeave),this._host.removeEventListener("wheel",this._onWheel),null!==this._chooseRDialog&&(this._chooseRDialog.close(),this._chooseRDialog=null),gn(this._nextAddCursorEl),this._nextAddCursorEl=null}}_handleMove(e){if(null!==this._panStart){let t=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),i=t.x-this._panStart.origin.x,n=t.y-this._panStart.origin.y;return this._editor.panTo({x:this._panStart.initialOffset.x+i,y:this._panStart.initialOffset.y+n}),void(this._panMoved=!0)}if(null!==this._atomDragState){let t=this._toModel(e),i=t.x-this._atomDragState.pointerDownModel.x,n=t.y-this._atomDragState.pointerDownModel.y,o=[];for(let e of this._atomDragState.atomIds){let t=this._atomDragState.initialPositions.get(e);void 0!==t&&o.push({atomId:e,p:{x:t.x+i,y:t.y+n}})}return this._editor.moveAtoms(o),void(this._atomDragMoved=!0)}let t=this._toModel(e),i=this._tester.test(t),n=i?.atom??null,o=i?.bond??null;if(null!==this._bondStart){this._bondDragMoved=!0;let e=null!==n&&n.id!==this._bondStart.id?n:null;this._editor.fire("bond:preview",{start:this._bondStart,cursor:t,candidate:e,kind:"hbond"===this._editor.getMode()?"hbond":"backbone"})}if(null!==this._hoverAtom&&(null===n||n.id!==this._hoverAtom.id)&&(this._editor.fire("monomer:hover-end",{atom:this._hoverAtom}),this._hoverAtom=null),null!==n&&(null===this._hoverAtom||this._hoverAtom.id!==n.id)&&(this._hoverAtom=n,this._editor.fire("monomer:hover",{atom:n,clientX:e.clientX,clientY:e.clientY,modelX:t.x,modelY:t.y})),null!==this._hoverBond&&(null===o||o.id!==this._hoverBond.id)&&(this._editor.fire("bond:hover-end",{bond:this._hoverBond}),this._hoverBond=null),null!==o&&(null===this._hoverBond||this._hoverBond.id!==o.id)&&(this._hoverBond=o,this._editor.fire("bond:hover",{bond:o,clientX:e.clientX,clientY:e.clientY})),null!==this._dragOrigin){let e=xn(this._dragOrigin,t);this._editor.fire("selection:rectangle-update",{rect:e})}this._updateNextAddCursor(e)}_handleClick(e){if(this._bondDragMoved)return void(this._bondDragMoved=!1);if(this._rectDragHappened)return void(this._rectDragHappened=!1);if(this._panMoved)return void(this._panMoved=!1);if(this._atomDragMoved)return void(this._atomDragMoved=!1);let t=this._toModel(e),i=this._tester.test(t),n=wn(e),o=this._editor.getMode();if("eraser"===o)return void 0!==i?.atom?void this._editor.removeAtom(i.atom):void 0!==i?.bond?void this._editor.removeBond(i.bond):void 0;if(void 0===i?.atom)if(void 0===i?.bond){if(this._addsEnabled()){let e=this._editor.getNextAddSymbol();if(null!==e)return void this._editor.addAtom(t,e.biotype,e.symbol)}!n.shift&&!n.ctrl&&!n.meta&&this._editor.clearSelection()}else this._editor.fire("bond:click",{bond:i.bond,modifiers:n});else{if("select"===o&&!n.ctrl&&!n.shift&&!n.meta){let e=this._editor.getNextAddSymbol();if(null!==e)return i.atom.biotype===e.biotype?void this._editor.replaceMonomer(i.atom,e.symbol):void this._editor.fire("editor:status",{message:`Cannot replace: ${i.atom.biotype} is incompatible with ${e.biotype}`,severity:"warn",durationMs:3e3})}this._editor.fire("monomer:click",{atom:i.atom,modifiers:n,clientX:e.clientX,clientY:e.clientY})}}_handleDblClick(e){let t=this._toModel(e),i=this._tester.test(t),n=wn(e);void 0===i?.atom?null===i&&this._editor.fitToContent():this._editor.fire("monomer:dblclick",{atom:i.atom,modifiers:n})}_handleContextMenu(e){this._enableContextMenu||e.preventDefault();let t=this._toModel(e),i=this._tester.test(t),n=()=>{e.preventDefault()};void 0!==i?.atom?this._editor.fire("monomer:contextmenu",{atom:i.atom,clientX:e.clientX,clientY:e.clientY,preventDefault:n}):void 0!==i?.bond&&this._editor.fire("bond:contextmenu",{bond:i.bond,clientX:e.clientX,clientY:e.clientY,preventDefault:n})}_handleMouseDown(e){if(0!==e.button)return;let t=this._toModel(e),i=this._tester.test(t),n=this._editor.getMode(),o=!0===e.ctrlKey||!0===e.metaKey,r=!0===e.shiftKey;if(void 0!==i?.atom){if("move"===n||"select"===n&&o){let e=this._editor.getSelection(),n=e.atoms.has(i.atom.id)?Array.from(e.atoms):[i.atom.id],o=this._editor.getMol(),r=new Map;for(let e of n){let t=o.atoms.find(t=>t.id===e);void 0!==t&&r.set(e,{x:t.p.x,y:t.p.y})}return this._atomDragState={atomIds:n,pointerDownModel:{x:t.x,y:t.y},initialPositions:r},void(this._atomDragMoved=!1)}return this._bondStart=i.atom,void(this._bondDragMoved=!1)}if(null===i){if("move"===n||"select"===n&&!r){let t=this._editor.getViewport();return this._panStart={origin:this._toViewBox({clientX:e.clientX,clientY:e.clientY}),initialOffset:{x:t.offset.x,y:t.offset.y}},void(this._panMoved=!1)}"select"===n&&r&&(this._dragOrigin=t,this._editor.fire("selection:rectangle-start",{origin:t}))}}_handleMouseUp(e){if(null!==this._panStart)return void(this._panStart=null);if(null!==this._atomDragState)return void(this._atomDragState=null);if(null!==this._bondStart){let t=this._bondStart,i=this._bondDragMoved;this._bondStart=null;let n=this._toModel(e),o=this._tester.test(n)?.atom;if(i&&void 0!==o&&o.id!==t.id){if(this._editor.fire("bond:preview-end",{start:t}),"hbond"===this._editor.getMode()){try{this._editor.addHydrogenBond(t,o)}catch{this._editor.fire("bond:cancel",{start:t})}return}let e=t.bio.chainId===o.bio.chainId&&vn(t,o,this._editor.getMol())?"backbone":"cross-polymer",i=_n(t,o,this._editor.getMol().bonds,e);if("fail"===i.mode)return this._editor.fire("bond:cancel",{start:t}),void this._editor.fire("editor:status",{message:i.reason,severity:"error",durationMs:3e3});if("auto"===i.mode){try{this._editor.addBond(t,o,i.r1,i.r2,i.kind)}catch{this._editor.fire("bond:cancel",{start:t})}return}return void this._openChooseR(t,o,e,i.freeR1,i.freeR2)}if(i){let e=this._addsEnabled()?this._editor.getNextAddSymbol():null;if(null!==e){let i;try{i=this._editor.addAtom(n,e.biotype,e.symbol)}catch{return this._editor.fire("bond:cancel",{start:t}),void this._editor.fire("bond:preview-end",{start:t})}let o=this._editor.getMol().atoms.find(e=>e.id===t.id);if(void 0===o)return this._editor.fire("bond:cancel",{start:t}),void this._editor.fire("bond:preview-end",{start:t});let r=o.bio.chainId===i.bio.chainId&&vn(o,i,this._editor.getMol())?"backbone":"cross-polymer",s=Oi(o,this._editor.getMol().bonds),a=Oi(i,this._editor.getMol().bonds);if(s.includes(2)&&a.includes(1)){try{this._editor.addBond(o,i,2,1,r)}catch{this._editor.fire("bond:cancel",{start:t})}return void this._editor.fire("bond:preview-end",{start:t})}let l=_n(o,i,this._editor.getMol().bonds,r);if("fail"===l.mode)return this._editor.fire("bond:cancel",{start:t}),this._editor.fire("editor:status",{message:l.reason,severity:"error",durationMs:3e3}),void this._editor.fire("bond:preview-end",{start:t});if("auto"===l.mode){try{this._editor.addBond(o,i,l.r1,l.r2,l.kind)}catch{this._editor.fire("bond:cancel",{start:t})}return void this._editor.fire("bond:preview-end",{start:t})}return this._editor.fire("bond:preview-end",{start:t}),void this._openChooseR(o,i,r,l.freeR1,l.freeR2)}return this._editor.fire("bond:cancel",{start:t}),void this._editor.fire("bond:preview-end",{start:t})}return}if(null===this._dragOrigin)return;let t=this._toModel(e),i=xn(this._dragOrigin,t);this._dragOrigin=null;let n=this._tester.testRect(i),o=Di.fromAtomsAndBonds(n.atoms.map(e=>e.id),n.bonds.map(e=>e.id)),r=Di.union(this._editor.getSelection(),o);this._editor.setSelection(r),this._editor.fire("selection:rectangle-end",{rect:i,selection:r}),this._rectDragHappened=!0,r.atoms.size>0&&"select"===this._editor.getMode()&&this._editor.setMode("move")}_handleMouseLeave(e){null!==this._hoverAtom&&(this._editor.fire("monomer:hover-end",{atom:this._hoverAtom}),this._hoverAtom=null),null!==this._hoverBond&&(this._editor.fire("bond:hover-end",{bond:this._hoverBond}),this._hoverBond=null),null!==this._bondStart&&(this._editor.fire("bond:cancel",{start:this._bondStart}),this._editor.fire("bond:preview-end",{start:this._bondStart}),this._bondStart=null,this._bondDragMoved=!1),this._dragOrigin=null,this._panStart=null,this._atomDragState=null,this._panMoved=!1,this._atomDragMoved=!1,gn(this._nextAddCursorEl)}_openChooseR(e,t,i,n,o){null===this._chooseRDialog&&(this._chooseRDialog=new pn(this._editor)),this._chooseRDialog.open(e,t,{freeR1:n,freeR2:o}).then(n=>{if(!this._destroyed){if(null===n)return void this._editor.fire("bond:cancel",{start:e});try{this._editor.addBond(e,t,n.r1,n.r2,i)}catch{this._editor.fire("bond:cancel",{start:e})}}})}_updateNextAddCursor(e){let t=this._editor.getNextAddSymbol(),i=this._editor.getMode(),n=null!==this._hoverAtom,o=null!==this._bondStart||null!==this._dragOrigin||null!==this._panStart||null!==this._atomDragState;if("select"!==i||null===t||n||o)return void(null!==this._nextAddCursorEl&&gn(this._nextAddCursorEl));let r=this._host.ownerDocument;if(null===r)return;null===this._nextAddCursorEl&&(this._nextAddCursorEl=function(e){let t="data-testid";for(let i=0;i<e.body.children.length;i++){let n=e.body.children[i];if(void 0!==n&&n.getAttribute(t)===bn)return n}let i=e.createElement("div");return i.className="hw-next-add-cursor",i.setAttribute(t,bn),i.style.display="none",e.body.appendChild(i),i}(r));let s=this._editor.getService().monomerLib,a=null;for(let e of s.getPolymerTypes()){let i=s.getMonomer(e,t.symbol);if(null!==i){a=i;break}}!function(e,t,i,n,o,r,s){let a=Gt({p:{x:0,y:0},biotype:i},o),l=te(n,i,o.colorTheme).background,h=q(l),d=t.length,c=d<=1?1:Math.min(1,2/d),u=`<svg xmlns="http://www.w3.org/2000/svg" viewBox="-28 -28 56 56" width="56" height="56" class="hw-next-add-cursor__svg" aria-hidden="true"><path d="${a}" fill="${l}" stroke="${l}" stroke-width="5" stroke-linejoin="round" stroke-linecap="round"/><text x="0" y="0" text-anchor="middle" dominant-baseline="central" font-family="Helvetica Neue, Helvetica, Arial, sans-serif" font-size="${o.fontSize*c}" fill="${h}">${function(e){let t="";for(let i=0;i<e.length;i++){let n=e.charAt(i);t+="<"===n?"&lt;":">"===n?"&gt;":"&"===n?"&amp;":n}return t}(t)}</text></svg>`;e.innerHTML=u;let p=e.style;p.left=r-28+"px",p.top=s-28+"px",p.display="block"}(this._nextAddCursorEl,t.symbol,t.biotype,a,this._editor._currentTheme(),e.clientX,e.clientY)}_addsEnabled(){return"select"===this._editor.getMode()}_handleWheel(e){let t=!0===e.ctrlKey||!0===e.metaKey;if(e.preventDefault(),t)return void this._wheelPan(e);let i=e.deltaY<0?1.1:1/1.1,n=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),o=this._editor.getViewport(),r=0===o.scale?n:{x:(n.x-o.offset.x)/o.scale,y:(n.y-o.offset.y)/o.scale};this._editor.zoom(i,r)}_wheelPan(e){let t=e.deltaX??0,i=e.deltaY??0;if(0===t&&0===i)return;let n=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),o=this._toViewBox({clientX:e.clientX+t,clientY:e.clientY+i}),r=o.x-n.x,s=o.y-n.y,a=this._editor.getViewport();this._editor.panTo({x:a.offset.x-r,y:a.offset.y-s})}_toModel(e){let t=this._host.querySelector("svg"),i=null!==t?t.querySelector(".hw-content"):null;if(null!==t&&null!==i){let t=yn(i,e.clientX,e.clientY);if(null!==t)return t;let n=this._host.getBoundingClientRect(),o=e.clientX-n.left,r=e.clientY-n.top,s=function(e){if(""===e)return null;let t,i=0,n=0,o=1,r=/(translate|scale)\(([^)]+)\)/g,s=!1;for(;null!==(t=r.exec(e));){s=!0;let e=t[1],r=(t[2]??"").split(/[,\s]+/).map(e=>Number(e)).filter(e=>Number.isFinite(e));"translate"===e?(i+=o*(r[0]??0),n+=o*(r[1]??0)):"scale"===e&&(o*=r[0]??1)}return s?{tx:i,ty:n,scale:o}:null}(i.getAttribute("transform")??"");return null!==s?{x:(o-s.tx)/(0===s.scale?1:s.scale),y:(r-s.ty)/(0===s.scale?1:s.scale)}:{x:o,y:r}}let n=this._host.getBoundingClientRect();return{x:e.clientX-n.left,y:e.clientY-n.top}}_toViewBox(e){let t=this._host.querySelector("svg");if(null!==t){let i=yn(t,e.clientX,e.clientY);if(null!==i)return i;let n=this._host.getBoundingClientRect(),o=e.clientX-n.left,r=e.clientY-n.top,s=function(e){if(null===e||""===e)return null;let t=e.split(/[,\s]+/).map(e=>Number(e)).filter(e=>Number.isFinite(e));if(t.length<4)return null;let i=t[2],n=t[3];return i<=0||n<=0?null:{w:i,h:n}}(t.getAttribute("viewBox"));return null!==s&&n.width>0&&n.height>0?{x:o*(s.w/n.width),y:r*(s.h/n.height)}:{x:o,y:r}}let i=this._host.getBoundingClientRect();return{x:e.clientX-i.left,y:e.clientY-i.top}}};function _n(e,t,i,n){let o=Fi(e),r=Fi(t);if(0===o||0===r)return{mode:"auto",r1:2,r2:1,kind:n};let s=Oi(e,i),a=Oi(t,i);return 0===s.length?{mode:"fail",reason:`${e.symbol} has no free R-groups (max ${o}).`}:0===a.length?{mode:"fail",reason:`${t.symbol} has no free R-groups (max ${r}).`}:s.includes(2)&&a.includes(1)&&(1===s.length||1===a.length)?{mode:"auto",r1:2,r2:1,kind:n}:1===s.length&&1===a.length?{mode:"auto",r1:s[0],r2:a[0],kind:n}:{mode:"choose",freeR1:s,freeR2:a}}function yn(e,t,i){let n=e;if("function"!=typeof n.getScreenCTM)return null;let o=n.getScreenCTM();if(null===o)return null;let r=null;try{let e=o;"function"==typeof e.inverse&&(r=e.inverse())}catch{return null}if(null===r)return null;let s=n.ownerSVGElement;if(null!=s&&"function"==typeof s.createSVGPoint){let e=s.createSVGPoint();e.x=t,e.y=i;let n=e.matrixTransform(r);return{x:n.x,y:n.y}}let a=r;return{x:a.a*t+a.c*i+a.e,y:a.b*t+a.d*i+a.f}}function vn(e,t,i){if(e.bio.chainId!==t.bio.chainId)return!1;let n=i.chains.find(t=>t.id===e.bio.chainId);if(void 0===n)return!1;let o=-1,r=-1;for(let i=0;i<n.backboneAtoms.length;i++){let s=n.backboneAtoms[i];s.id===e.id&&(o=i),s.id===t.id&&(r=i)}return!(o<0||r<0)&&1===Math.abs(o-r)}function wn(e){return{shift:!0===e.shiftKey,alt:!0===e.altKey,ctrl:!0===e.ctrlKey,meta:!0===e.metaKey}}function xn(e,t){return{x:Math.min(e.x,t.x),y:Math.min(e.y,t.y),width:Math.abs(e.x-t.x),height:Math.abs(e.y-t.y)}}var Cn=class{constructor(e,t,i){this._destroyed=!1,this._host=e,this._editor=t,this._enabled=!1!==i?.enableKeyboard,this._enabled&&null===e.getAttribute("tabindex")&&e.setAttribute("tabindex","0"),this._onKey=e=>this._handleKey(e),e.addEventListener("keydown",this._onKey)}destroy(){this._destroyed||(this._destroyed=!0,this._host.removeEventListener("keydown",this._onKey))}_handleKey(e){if(!this._enabled)return;let t=this._classify(e),i={shift:!0===(n=e).shiftKey,alt:!0===n.altKey,ctrl:!0===n.ctrlKey,meta:!0===n.metaKey};var n;if(null===t)return void this._editor.fire("key:unhandled",{key:e.key,modifiers:i,preventDefault:()=>e.preventDefault()});let o=!1;this._editor.fire("key:command",{command:t,preventDefault:()=>{o=!0,e.preventDefault()}}),!o&&(e.preventDefault(),"clearSelection"!==t&&(e.stopPropagation(),e.stopImmediatePropagation?.()),this._execute(t))}_classify(e){let t=e.key,i=e.ctrlKey||e.metaKey;return"Delete"===t||"Backspace"===t?"delete":!i||"z"!==t&&"Z"!==t||e.shiftKey?i&&(("z"===t||"Z"===t)&&e.shiftKey||"y"===t||"Y"===t)?"redo":!i||"a"!==t&&"A"!==t?!i||"c"!==t&&"C"!==t?!i||"v"!==t&&"V"!==t?!i||"x"!==t&&"X"!==t?"Escape"===t?"clearSelection":"+"===t||"="===t?"zoomIn":"-"===t||"_"===t?"zoomOut":"0"===t?"fitToContent":"ArrowUp"===t?"nudgeUp":"ArrowDown"===t?"nudgeDown":"ArrowLeft"===t?"nudgeLeft":"ArrowRight"===t?"nudgeRight":null:"cut":"paste":"copy":"selectAll":"undo"}_execute(e){switch(e){case"delete":return void this._editor.deleteSelection();case"undo":return void this._editor.undo();case"redo":return void this._editor.redo();case"selectAll":return void this._editor.selectAll();case"clearSelection":return void this._editor.clearSelection();case"zoomIn":return void this._editor.zoom(1.1);case"zoomOut":return void this._editor.zoom(1/1.1);case"fitToContent":return void this._editor.fitToContent();case"nudgeUp":return void this._editor.nudgeSelection(0,-5);case"nudgeDown":return void this._editor.nudgeSelection(0,5);case"nudgeLeft":return void this._editor.nudgeSelection(-5,0);case"nudgeRight":return void this._editor.nudgeSelection(5,0);case"copy":{let e=this._editor.getHelm();return void this._editor.fire("clipboard:copy",{format:"helm",payload:e})}case"cut":{let e=this._editor.getHelm();return this._editor.fire("clipboard:copy",{format:"helm",payload:e}),void this._editor.deleteSelection()}case"paste":return void this._editor.fire("clipboard:paste",{format:"helm"});default:return}}},kn=class{constructor(e,t){this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._destroyed=!1,this._unsubs=[],this._host=e,this._editor=t,this._tester=new Yi(t.getMol(),t._currentTheme()),this._unsubs.push(t.on("mol:changed",()=>{this._tester=new Yi(this._editor.getMol(),this._editor._currentTheme())})),this._onDragOver=e=>this._handleDragOver(e),this._onDrop=e=>this._handleDrop(e),this._onDragStart=e=>this._handleDragStart(e),this._onDragEnd=e=>this._handleDragEnd(e),this._onDragEnter=e=>this._handleDragEnter(e),this._onDragLeave=e=>this._handleDragLeave(e),e.addEventListener("dragover",this._onDragOver),e.addEventListener("drop",this._onDrop),e.addEventListener("dragstart",this._onDragStart),e.addEventListener("dragend",this._onDragEnd),e.addEventListener("dragenter",this._onDragEnter),e.addEventListener("dragleave",this._onDragLeave)}startPaletteDrag(e,t){this._currentPaletteSymbol=e,this._currentPaletteBiotype=t,this._editor.fire("dnd:start",{source:"palette",symbol:e})}cancelPaletteDrag(){null!==this._currentPaletteSymbol&&(this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._editor.fire("dnd:cancel",{source:"palette"}))}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();this._host.removeEventListener("dragover",this._onDragOver),this._host.removeEventListener("drop",this._onDrop),this._host.removeEventListener("dragstart",this._onDragStart),this._host.removeEventListener("dragend",this._onDragEnd),this._host.removeEventListener("dragenter",this._onDragEnter),this._host.removeEventListener("dragleave",this._onDragLeave)}}_activePaletteSymbol(e){if(null!==this._currentPaletteSymbol&&null!==this._currentPaletteBiotype)return{symbol:this._currentPaletteSymbol,biotype:this._currentPaletteBiotype};let t=e.dataTransfer;if(null==t)return null;try{let e="function"==typeof t.getData?t.getData("application/x-hwe-monomer"):"";if(""===e)return null;let i=JSON.parse(e);return"string"!=typeof i.symbol||"string"!=typeof i.biotype?null:{symbol:i.symbol,biotype:i.biotype}}catch{return null}}_handleDragEnter(e){if(null!==this._activePaletteSymbol(e)&&(e.preventDefault(),null!==e.dataTransfer&&void 0!==e.dataTransfer))try{e.dataTransfer.dropEffect="copy"}catch{}}_handleDragLeave(e){}_handleDragOver(e){if(null===this._activePaletteSymbol(e))return;if(e.preventDefault(),null!==e.dataTransfer&&void 0!==e.dataTransfer)try{e.dataTransfer.dropEffect="copy"}catch{}let t=this._toModel(e),i=this._tester.test(t),n=void 0!==i?.atom?i.atom:void 0!==i?.bond?i.bond:void 0,o={clientX:e.clientX,clientY:e.clientY};void 0!==n&&(o.target=n),this._editor.fire("dnd:over",o)}_handleDrop(e){let t=this._activePaletteSymbol(e);if(null===t)return;e.preventDefault();let{symbol:i,biotype:n}=t,o=this._toModel(e),r=this._tester.test(o),s=void 0!==r?.atom?r.atom:void 0!==r?.bond?r.bond:void 0,a={symbol:i,biotype:n,clientX:e.clientX,clientY:e.clientY};void 0!==s&&(a.target=s),this._editor.fire("dnd:drop",a),void 0!==r?.atom?this._editor.replaceMonomer(r.atom,i):this._editor.addAtom(o,n,i),this._currentPaletteSymbol=null,this._currentPaletteBiotype=null}_handleDragStart(e){this._editor.fire("dnd:start",{source:"canvas"})}_handleDragEnd(e){null!==this._currentPaletteSymbol&&(this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._editor.fire("dnd:cancel",{source:"palette"}))}_toModel(e){let t=this._host.querySelector("svg"),i=null!==t?t.querySelector(".hw-content"):null;if(null!==t&&null!==i){let t=function(e,t,i){let n=e;if("function"!=typeof n.getScreenCTM)return null;let o=n.getScreenCTM();if(null===o)return null;let r=null;try{let e=o;"function"==typeof e.inverse&&(r=e.inverse())}catch{return null}if(null===r)return null;let s=n.ownerSVGElement;if(null!=s&&"function"==typeof s.createSVGPoint){let e=s.createSVGPoint();e.x=t,e.y=i;let n=e.matrixTransform(r);return{x:n.x,y:n.y}}let a=r;return{x:a.a*t+a.c*i+a.e,y:a.b*t+a.d*i+a.f}}(i,e.clientX,e.clientY);if(null!==t)return t;let n=this._host.getBoundingClientRect(),o=e.clientX-n.left,r=e.clientY-n.top,s=function(e){if(""===e)return null;let t,i=0,n=0,o=1,r=/(translate|scale)\(([^)]+)\)/g,s=!1;for(;null!==(t=r.exec(e));){s=!0;let e=t[1],r=(t[2]??"").split(/[,\s]+/).map(e=>Number(e)).filter(e=>Number.isFinite(e));"translate"===e?(i+=o*(r[0]??0),n+=o*(r[1]??0)):"scale"===e&&(o*=r[0]??1)}return s?{tx:i,ty:n,scale:o}:null}(i.getAttribute("transform")??"");return null!==s?{x:(o-s.tx)/(0===s.scale?1:s.scale),y:(r-s.ty)/(0===s.scale?1:s.scale)}:{x:o,y:r}}let n=this._host.getBoundingClientRect();return{x:e.clientX-n.left,y:e.clientY-n.top}}},En=class{constructor(e,t){this._modal=null,this._atom=null,this._editor=e;let i=e._getHost();if(null===i)throw new Error("AtomPropsDialog: editor has no host element.");this._doc=t?.documentImpl??Xi(i)}get isOpen(){return null!==this._modal&&this._modal.isOpen}open(e){this.close(),this._atom=e;let t=this._editor._getHost();if(null===t)return;let i=new hn(t,{documentImpl:this._doc,title:"Monomer Properties",testId:"atom-props"});this._modal=i;let n=Qi(this._doc,"div",{class:"hw-modal__info"},[`Position ${e.bio.continuousId} in ${e.bio.chainId}`]),o=dn(this._doc,"Symbol",e.symbol,"atom-props-symbol"),r=dn(this._doc,"Annotation",e.bio.annotation??"","atom-props-annotation"),s=un(this._doc,"atom-props"),a=()=>this._commit(o.input.value,r.input.value);s.ok.addEventListener("click",a),s.cancel.addEventListener("click",()=>this.close()),i.setPrimaryAction(a),i.body.appendChild(n),i.body.appendChild(o.row),i.body.appendChild(r.row),i.body.appendChild(s.row),i.open()}close(){null!==this._modal&&(this._modal.close(),this._modal=null),this._atom=null}_commit(e,t){let i=this._atom;if(null===i)return void this.close();let n=e.trim(),o=(i.bio.annotation??"")!==t;if(n.length>0&&n!==i.symbol&&this._editor.replaceMonomer(i,n),o){let e=new qi(this._editor.getMol()),n={};n.tag=""===t?void 0:t,e.updateAtom(i.id,n);let{mol:o}=e.commit();this._editor.setMol(o);let r=o.atoms.find(e=>e.id===i.id);if(void 0!==r){let e={atom:r};void 0!==i.bio.annotation&&(e.oldAnnotation=i.bio.annotation),""!==t&&(e.newAnnotation=t),this._editor.fire("monomer:annotate",e)}}this.close()}},Bn=class{constructor(e,t){this._modal=null,this._bond=null,this._editor=e;let i=e._getHost();if(null===i)throw new Error("BondPropsDialog: editor has no host element.");this._doc=t?.documentImpl??Xi(i)}get isOpen(){return null!==this._modal&&this._modal.isOpen}open(e){this.close(),this._bond=e;let t=this._editor._getHost();if(null===t)return;let i=new hn(t,{documentImpl:this._doc,title:"Bond Properties",testId:"bond-props"});this._modal=i;let n=Qi(this._doc,"div",{class:"hw-modal__info"},[`Kind: ${e.kind}`]),o=this._buildAtomsPreviewRow(e),r="numeric"===e.r1.kind,s="numeric"===e.r2.kind,a=r&&s,l=this._editor.getMol().bonds,h=a?Sn(e.r1,e.a1,l):[],d=a?Sn(e.r2,e.a2,l):[],c=null,u=null;if(a){let t=String(e.r1.r),i=String(e.r2.r);c=cn(this._doc,`R-group on ${e.a1.symbol} (${e.a1.bio.chainId}:${e.a1.bio.positionInChain})`,h,t,"bond-props-r1"),u=cn(this._doc,`R-group on ${e.a2.symbol} (${e.a2.bio.chainId}:${e.a2.bio.positionInChain})`,d,i,"bond-props-r2")}let p=un(this._doc,"bond-props"),m=()=>{let t=null!==c?Number(Mn(c.select,e.r1.r)):null,i=null!==u?Number(Mn(u.select,e.r2.r)):null;this._commit(t,i)};p.ok.addEventListener("click",m),p.cancel.addEventListener("click",()=>this.close()),i.setPrimaryAction(m),i.body.appendChild(n),null!==o&&i.body.appendChild(o),null!==c&&i.body.appendChild(c.row),null!==u&&i.body.appendChild(u.row),i.body.appendChild(p.row),i.open()}_buildAtomsPreviewRow(e){let t=this._rdkit(),i=this._buildAtomCell(e.a1,t,"bond-props-atom-a1"),n=this._buildAtomCell(e.a2,t,"bond-props-atom-a2"),o=Qi(this._doc,"div",{class:"hw-bond-props__bond-arrow"},["↔"]);return Qi(this._doc,"div",{class:"hw-bond-props__atoms","data-testid":"bond-props-atoms"},[i,o,n])}_buildAtomCell(e,t,i){let n=e.monomer?.name??e.symbol,o=e.symbol===n?e.symbol:`${e.symbol} — ${n}`,r=Qi(this._doc,"div",{class:"hw-bond-props__atom-label"},[o]),s={class:"hw-bond-props__atom-rdkit","data-testid":`${i}-rdkit`},a=Qi(this._doc,"div",s),l=e.monomer?.smiles;if(null!==t&&void 0!==l&&""!==l){let e=Zi(t,l,220,140);null!==e&&""!==e&&(a.innerHTML=e)}return Qi(this._doc,"div",{class:"hw-bond-props__atom","data-testid":i},[r,a])}_rdkit(){let e=this._editor.getService().options?.rdkitModule;return e??null}close(){null!==this._modal&&(this._modal.close(),this._modal=null),this._bond=null}_commit(e,t){let i=this._bond;if(null===i)return void this.close();let n="numeric"===i.r1.kind?i.r1.r:null,o="numeric"===i.r2.kind?i.r2.r:null;if(null===e||null===t||e===n&&t===o)this.close();else{if(null!==e&&null!==t){let r=i.kind,s=i.a1,a=i.a2;this._editor.removeBond(i);try{this._editor.addBond(s,a,e,t,r)}catch(e){if(null!==n&&null!==o)try{this._editor.addBond(s,a,n,o,i.kind)}catch{}}}this.close()}}};function Sn(e,t,i){let n=t.monomer?.rgroups;if(void 0===n||0===n.length)return[{value:"1",label:"R1"},{value:"2",label:"R2"},{value:"3",label:"R3"}];let o=new Set(Oi(t,i));o.add(e.r);let r=Array.from(o).sort((e,t)=>e-t),s=[];for(let e of r){let t=n[e-1];if(void 0===t)continue;let i=void 0!==t.capGroupName&&""!==t.capGroupName?` (${t.capGroupName})`:"";s.push({value:String(e),label:`${t.label}${i}`})}return s}function Mn(e,t){let i=e.value;if("string"==typeof i&&i.length>0){let e=Number(i);if(Number.isFinite(e)&&e>=1)return e}let n=e.querySelectorAll("option");for(let e of Array.from(n))if(null!==e.getAttribute("selected")){let t=e.getAttribute("value")??"",i=Number(t);if(Number.isFinite(i)&&i>=1)return i}return t}var Tn=class{constructor(e,t){this._modal=null,this._result=null,this._findInput=null,this._replaceInput=null,this._matches=[],this._cursor=-1,this._editor=e;let i=e._getHost();if(null===i)throw new Error("FindReplaceDialog: editor has no host element.");this._doc=t?.documentImpl??Xi(i)}get isOpen(){return null!==this._modal&&this._modal.isOpen}open(){this.close();let e=this._editor._getHost();if(null===e)return;let t=new hn(e,{documentImpl:this._doc,title:"Find / Replace",testId:"find-replace"});this._modal=t;let i=dn(this._doc,"Find","","find-replace-find"),n=dn(this._doc,"Replace with","","find-replace-replace");this._findInput=i.input,this._replaceInput=n.input;let o=this._doc.createElement("button");o.setAttribute("class","hw-modal__find-next"),o.setAttribute("type","button"),o.setAttribute("data-testid","find-replace-next"),o.appendChild(this._doc.createTextNode("Find Next")),o.addEventListener("click",()=>this._findNext());let r=this._doc.createElement("button");r.setAttribute("class","hw-modal__replace"),r.setAttribute("type","button"),r.setAttribute("data-testid","find-replace-replace-one"),r.appendChild(this._doc.createTextNode("Replace")),r.addEventListener("click",()=>this._replaceOne());let s=this._doc.createElement("button");s.setAttribute("class","hw-modal__replace-all"),s.setAttribute("type","button"),s.setAttribute("data-testid","find-replace-replace-all"),s.appendChild(this._doc.createTextNode("Replace All")),s.addEventListener("click",()=>this._replaceAll());let a=this._doc.createElement("button");a.setAttribute("class","hw-modal__cancel"),a.setAttribute("type","button"),a.setAttribute("data-testid","find-replace-close"),a.appendChild(this._doc.createTextNode("Close")),a.addEventListener("click",()=>this.close());let l=Qi(this._doc,"div",{class:"hw-modal__actions"},[o,r,s,a]),h=Qi(this._doc,"div",{class:"hw-modal__result","data-testid":"find-replace-result"},["0 matches"]);this._result=h,t.setPrimaryAction(()=>this._findNext()),t.body.appendChild(i.row),t.body.appendChild(n.row),t.body.appendChild(l),t.body.appendChild(h),t.open()}close(){null!==this._modal&&(this._modal.close(),this._modal=null),this._result=null,this._findInput=null,this._replaceInput=null,this._matches=[],this._cursor=-1}_findNext(){let e=this._findInput?.value.trim()??"";if(""===e)return void this._setResultText("Enter a symbol to find");let t=this._editor.findMonomers(e);if(this._matches=t.map(e=>e.id),0===this._matches.length)return this._cursor=-1,this._editor.setHighlights([]),void this._setResultText("No matches");this._cursor=(this._cursor+1)%this._matches.length;let i=this._matches[this._cursor];void 0!==i&&this._editor.setHighlights([i]),this._setResultText(`${this._cursor+1} / ${this._matches.length} matches`)}_replaceOne(){let e=this._findInput?.value.trim()??"",t=this._replaceInput?.value.trim()??"";if(""===e||""===t)return void this._setResultText("Both Find and Replace fields are required");if(0===this._matches.length||this._cursor<0)return void this._findNext();let i=this._matches[this._cursor];if(void 0===i)return;let n=this._editor.getMol().atoms.find(e=>e.id===i);if(void 0!==n)if(this._editor.replaceMonomer(n,t),this._matches.splice(this._cursor,1),0===this._matches.length)this._cursor=-1,this._editor.setHighlights([]),this._setResultText("Replaced; no further matches");else{this._cursor=this._cursor%this._matches.length;let e=this._matches[this._cursor];void 0!==e&&this._editor.setHighlights([e]),this._setResultText(`${this._matches.length} matches remaining`)}}_replaceAll(){let e=this._findInput?.value.trim()??"",t=this._replaceInput?.value.trim()??"";if(""===e||""===t)return void this._setResultText("Both Find and Replace fields are required");let i=this._editor.replaceMonomers(e,t);this._matches=[],this._cursor=-1,this._editor.setHighlights([]),this._setResultText(`${i} replacement${1===i?"":"s"} made`)}_setResultText(e){if(null!==this._result){for(;null!==this._result.firstChild;)this._result.removeChild(this._result.firstChild);this._result.appendChild(this._doc.createTextNode(e))}}},In=Object.freeze(new Set),Ln=class{constructor(e,t){if(this._events=new Ui,this._destroyed=!1,this._view=null,this._pointer=null,this._keyboard=null,this._dnd=null,this._atomDialog=null,this._bondDialog=null,this._findReplaceDialog=null,this._viewBootstrapped=!1,this._mode="select",this._nextAdd=null,this._lastAction=null,this._lastTripletSugarPos=null,void 0===t.service||null===t.service)throw new TypeError("HelmEditor: options.service is required");this._host=e,this._service=t.service,this._options=Object.freeze({...t}),this._mol=b(),this._selection=Di.empty(),this._highlights=In,this._theme=t.service.theme??Dt,this._viewport={scale:1,offset:{x:0,y:0}},this._viewOnly=t.viewOnly??!1,this._history=new Ki({maxEntries:100}),this._history.push({mol:this._mol,label:"initial"}),this._libUnsub=this._service.monomerLib.onChanged.subscribe(e=>{let t=this._service.monomerLib,i="number"==typeof t.version?t.version:0,n="reload"===e.type?"replace":"update";this._events.fire("monomer-lib:change",{source:this._service.monomerLib.source,version:i,reason:n})}),void 0!==t.initialHelm&&this.setHelm(t.initialHelm),this._bootstrapWaveB()}_bootstrapWaveB(){if(this._viewBootstrapped||null===this._host)return;let e=this._resolveDocument(this._host);if(null===e)return;this._viewBootstrapped=!0;let t={documentImpl:e};void 0!==this._options.width&&(t.width=this._options.width),void 0!==this._options.height&&(t.height=this._options.height),this._view=new sn(this._host,this,t),!0!==this._viewOnly&&(this._pointer=new An(this._host,this,{enableContextMenu:this._options.enableContextMenu??!0})),!1!==this._options.enableKeyboard&&(this._keyboard=new Cn(this._host,this,{enableKeyboard:!0})),!1!==this._options.enableDragDrop&&(this._dnd=new kn(this._host,this)),this._events.on("monomer:hover",e=>{this.setHighlights([e.atom.id])}),this._events.on("monomer:hover-end",()=>{this.clearHighlights()}),this._events.on("monomer:click",e=>{let t=e.modifiers;!0!==t.ctrl&&!0!==t.meta?!0!==t.shift?this.setSelection(Di.fromAtoms([e.atom.id])):this.setSelection(Di.union(this._selection,Di.fromAtoms([e.atom.id]))):this.setSelection(Di.toggle(this._selection,{kind:"atom",id:e.atom.id}))})}_resolveDocument(e){let t=e.ownerDocument;if(null!=t)return t;let i=globalThis;return void 0!==i.document?i.document:null}destroy(){this._destroyed||(this._destroyed=!0,null!==this._atomDialog&&(this._atomDialog.close(),this._atomDialog=null),null!==this._bondDialog&&(this._bondDialog.close(),this._bondDialog=null),null!==this._findReplaceDialog&&(this._findReplaceDialog.close(),this._findReplaceDialog=null),null!==this._dnd&&(this._dnd.destroy(),this._dnd=null),null!==this._keyboard&&(this._keyboard.destroy(),this._keyboard=null),null!==this._pointer&&(this._pointer.destroy(),this._pointer=null),null!==this._view&&(this._view.destroy(),this._view=null),this._libUnsub(),this._events.clear(),this._history.clear())}resize(e,t){this._ensureLive(),null!==this._view&&this._view.resize(e,t),this._events.fire("view:resize",{width:e,height:t})}redraw(){this._ensureLive(),null===this._view?this._events.fire("render:skip",{reason:"no-view-mounted"}):this._view.redraw()}setHelm(e,t){this._ensureLive();let i=t?.canonicalize??this._options.canonicalize??!1,n=this._service.parse(e,{mode:"lenient"}),o=n.diagnostics;o.filter(e=>"error"===e.severity).length>0&&this._events.fire("helm:parse-error",{helm:e,diagnostics:o});for(let e of o)"error"===e.severity?this._events.fire("validation:error",{diagnostic:e}):"warning"===e.severity&&this._events.fire("validation:warning",{diagnostic:e});let r=n.mol;if(i){let t=this._service.canonicalize(e);r=this._service.parse(t,{mode:"lenient"}).mol}let s=Et(r,this._layoutOptions());return this._replaceMol(s,"setHelm","api"),{mol:s,diagnostics:o}}getHelm(e){this._ensureLive();let t={};return void 0!==e?.canonicalize&&(t.canonicalize=e.canonicalize),void 0!==e?.includeHighlights&&(t.includeHighlights=e.includeHighlights),this._service.serialize(this._mol,t)}setMol(e){this._ensureLive(),this._replaceMol(e,"setMol","api")}getMol(){return this._mol}getService(){return this._service}getSelection(){return this._selection}setSelection(e){if(this._ensureLive(),Di.equals(this._selection,e))return;let t=Di.difference(e,this._selection),i=Di.difference(this._selection,e);this._selection=e,this._events.fire("selection:change",{selection:e,addedAtomIds:t.atoms,removedAtomIds:i.atoms,addedBondIds:t.bonds,removedBondIds:i.bonds})}selectAll(){this._ensureLive();let e=this._mol.atoms.map(e=>e.id),t=this._mol.bonds.map(e=>e.id);this.setSelection(Di.fromAtomsAndBonds(e,t))}clearSelection(){this._ensureLive(),!this._selection.isEmpty&&this.setSelection(Di.empty())}setHighlights(e){this._ensureLive();let t=new Set(e);this._highlights=t,this._events.fire("highlight:change",{atomIds:t,bondIds:In})}clearHighlights(){this._ensureLive(),0!==this._highlights.size&&(this._highlights=In,this._events.fire("highlight:change",{atomIds:In,bondIds:In}))}addAtom(e,t,i){this._ensureLive();let n=new qi(this._mol),o=n.addAtom({p:e,biotype:t,symbol:i}),{mol:r}=n.commit(),s=oe(r,this._service.monomerLib,{mode:"lenient"}).mol;this._replaceMol(s,`addAtom:${i}`,"api");let a=g(s,o);if(void 0===a)throw new Error("HelmEditor.addAtom: lost atom after commit");return this._events.fire("monomer:add",{atom:a,source:"api"}),a}removeAtom(e){this._ensureLive();let t="number"==typeof e?e:e.id,i=g(this._mol,t);if(void 0===i)return;let n=new qi(this._mol);n.removeAtom(t);let{mol:o}=n.commit();this._replaceMol(o,`removeAtom:${i.symbol}`,"api"),this._events.fire("monomer:remove",{atom:i,source:"api"})}addBond(e,t,i,n,r){let s,a;this._ensureLive();try{this._validateAddBondConstraints(e,t,i,n);let o=r??"backbone",l=this._maybeMergeForLinearExtend(e,t,i,n,o);if(null!==l)({id:s,mol:a}=l);else{let o=new qi(this._mol);s=o.addBond({a1:e.id,a2:t.id,kind:r??"backbone",r1:{kind:"numeric",r:i},r2:{kind:"numeric",r:n}}),({mol:a}=o.commit())}}catch(r){let s=r instanceof o?r.message:this._friendlyBondError(r instanceof Error?r.message:String(r),e,t,i,n);throw this._events.fire("editor:status",{message:`Could not add bond: ${s}`,severity:"error",durationMs:3e3}),r}this._replaceMol(a,"addBond","api");let l=A(a,s);if(void 0===l)throw new Error("HelmEditor.addBond: lost bond after commit");return this._events.fire("bond:add",{bond:l,source:"api"}),l}_maybeMergeForLinearExtend(e,t,i,n,o){if(e.bio.chainId===t.bio.chainId||"backbone"!==o&&"cross-polymer"!==o)return null;let r=this._mol.chains.find(t=>t.id===e.bio.chainId),s=this._mol.chains.find(e=>e.id===t.bio.chainId);if(void 0===r||void 0===s||r.polymerType!==s.polymerType||r.polymerType===B.CHEM||r.polymerType===B.BLOB)return null;if(2===i&&1===n){let i=r.backboneAtoms[r.backboneAtoms.length-1],n=s.backboneAtoms[0];if(void 0!==i&&void 0!==n&&i.id===e.id&&n.id===t.id)return this._mergeChains(r,s,o)}if(1===i&&2===n){let i=r.backboneAtoms[0],n=s.backboneAtoms[s.backboneAtoms.length-1];if(void 0!==i&&void 0!==n&&i.id===e.id&&n.id===t.id)return this._mergeChains(s,r,o)}return null}_mergeChains(e,t,i){let n=e.backboneAtoms.length,o=new Set;for(let e of t.backboneAtoms)o.add(e.id),void 0!==e.branchAtom&&o.add(e.branchAtom.id);let r=new Map,s=n;for(let i of t.backboneAtoms){s+=1;let t={...i,bio:{...i.bio,chainId:e.id,positionInChain:s}};if(r.set(i.id,t),void 0!==i.branchAtom){let t=i.branchAtom,n={...t,bio:{...t.bio,chainId:e.id,positionInChain:s}};r.set(t.id,n)}}for(let e of t.backboneAtoms){let t=r.get(e.id);if(void 0===t||void 0===e.branchAtom)continue;let i=r.get(e.branchAtom.id);void 0!==i&&(t.branchAtom=i)}for(let e of this._mol.atoms)r.has(e.id)||r.set(e.id,e);let a=0;for(let e of this._mol.atoms)e.id>a&&(a=e.id);for(let e of this._mol.bonds)e.id>a&&(a=e.id);let l=a+1,h={id:l,a1:r.get(e.backboneAtoms[e.backboneAtoms.length-1].id),a2:r.get(t.backboneAtoms[0].id),kind:"backbone",r1:{kind:"numeric",r:2},r2:{kind:"numeric",r:1}},d=[];for(let e of this._mol.bonds){let t=r.get(e.a1.id)??e.a1,i=r.get(e.a2.id)??e.a2;t===e.a1&&i===e.a2?d.push(e):d.push({...e,a1:t,a2:i})}d.push(h);let c=[],u=[...e.backboneAtoms];for(let e of t.backboneAtoms)u.push(r.get(e.id));for(let i of this._mol.chains)if(i.id!==t.id)if(i.id===e.id){let e=i.bonds.map(e=>{let t=r.get(e.a1.id)??e.a1,i=r.get(e.a2.id)??e.a2;return t===e.a1&&i===e.a2?e:{...e,a1:t,a2:i}});for(let i of t.bonds){let t=r.get(i.a1.id)??i.a1,n=r.get(i.a2.id)??i.a2;e.push(t===i.a1&&n===i.a2?i:{...i,a1:t,a2:n})}e.push(h),c.push({id:i.id,polymerType:i.polymerType,backboneAtoms:u,bonds:e,...void 0!==i.annotation?{annotation:i.annotation}:{}})}else{let e=i.backboneAtoms.map(e=>r.get(e.id)??e),t=i.bonds.map(e=>{let t=r.get(e.a1.id)??e.a1,i=r.get(e.a2.id)??e.a2;return t===e.a1&&i===e.a2?e:{...e,a1:t,a2:i}});c.push({id:i.id,polymerType:i.polymerType,backboneAtoms:e,bonds:t,...void 0!==i.annotation?{annotation:i.annotation}:{}})}let p={atoms:this._mol.atoms.map(e=>r.get(e.id)??e),bonds:d,chains:c,groups:this._mol.groups,annotations:this._mol.annotations};return p=this._refreshContinuousIdsLocal(p),{id:l,mol:p}}_refreshContinuousIdsLocal(e){let t=M(e),i=new Map;for(let n of e.atoms){let e=t.get(n.id);void 0!==e&&e!==n.bio.continuousId?i.set(n.id,{...n,bio:{...n.bio,continuousId:e}}):i.set(n.id,n)}for(let t of e.atoms){if(void 0===t.branchAtom)continue;let e=i.get(t.id),n=i.get(t.branchAtom.id);void 0===e||void 0===n||(e.branchAtom=n)}let n=e.bonds.map(e=>{let t=i.get(e.a1.id)??e.a1,n=i.get(e.a2.id)??e.a2;return t===e.a1&&n===e.a2?e:{...e,a1:t,a2:n}}),o=new Map;for(let e of n)o.set(e.id,e);let r=e.chains.map(e=>{let t=e.backboneAtoms.map(e=>i.get(e.id)??e),n=e.bonds.map(e=>o.get(e.id)??e);return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:n,...void 0!==e.annotation?{annotation:e.annotation}:{}}});return{atoms:e.atoms.map(e=>i.get(e.id)??e),bonds:n,chains:r,groups:e.groups,annotations:e.annotations}}_friendlyBondError(e,t,i,n,o){return e.includes("duplicate bond")?`bond ${t.symbol}:R${n} ↔ ${i.symbol}:R${o} already exists`:e.includes("does not exist")?"one of the endpoint atoms is missing":e}_validateAddBondConstraints(e,t,i,n){let r=this._mol.bonds,s=Fi(e);if(s>0&&(i<1||i>s))throw new o("rgroup-not-on-monomer",`R-group R${i} is not defined on monomer '${e.symbol}' (has R1..R${s})`,{atomId:e.id,requested:i,total:s});let a=Fi(t);if(a>0&&(n<1||n>a))throw new o("rgroup-not-on-monomer",`R-group R${n} is not defined on monomer '${t.symbol}' (has R1..R${a})`,{atomId:t.id,requested:n,total:a});if(s>0){let t=zi(e,r).find(e=>e.rNumber===i);if(void 0!==t){let n="r1"===t.side?t.bond.a2:t.bond.a1;throw new o("rgroup-already-bonded",`R-group R${i} on '${e.symbol}' is already bonded to '${n.symbol}' (${n.bio.chainId}:${n.bio.positionInChain})`,{atomId:e.id,requested:i,conflictingBondId:t.bond.id})}}if(a>0){let e=zi(t,r).find(e=>e.rNumber===n);if(void 0!==e){let i="r1"===e.side?e.bond.a2:e.bond.a1;throw new o("rgroup-already-bonded",`R-group R${n} on '${t.symbol}' is already bonded to '${i.symbol}' (${i.bio.chainId}:${i.bio.positionInChain})`,{atomId:t.id,requested:n,conflictingBondId:e.bond.id})}}for(let s of r){if("numeric"!==s.r1.kind||"numeric"!==s.r2.kind)continue;let r=s.a1.id===e.id&&s.a2.id===t.id&&s.r1.r===i&&s.r2.r===n,a=s.a1.id===t.id&&s.a2.id===e.id&&s.r1.r===n&&s.r2.r===i;if(r||a)throw new o("duplicate-bond",`bond ${e.symbol}:R${i} ↔ ${t.symbol}:R${n} already exists`,{atomId:e.id,bondId:s.id})}}_freeRgroupsOn(e){return Oi(e,this._mol.bonds)}addHydrogenBond(e,t){this._ensureLive();let i=new qi(this._mol),n={kind:"pair"},o=i.addBond({a1:e.id,a2:t.id,kind:"hbond",r1:n,r2:n}),{mol:r}=i.commit();this._replaceMol(r,"addHydrogenBond","api");let s=A(r,o);if(void 0===s)throw new Error("HelmEditor.addHydrogenBond: lost bond after commit");return this._events.fire("bond:add",{bond:s,source:"api"}),s}removeBond(e){this._ensureLive();let t="number"==typeof e?e:e.id,i=A(this._mol,t);if(void 0===i)return;let n=new qi(this._mol);n.removeBond(t);let{mol:o}=n.commit();this._replaceMol(o,"removeBond","api"),this._events.fire("bond:remove",{bond:i,source:"api"})}replaceMonomer(e,t){this._ensureLive();let i=g(this._mol,e.id);if(void 0===i)return;let n=i.symbol;if(n===t)return;let o=new qi(this._mol);o.updateAtom(e.id,{symbol:t});let{mol:r}=o.commit(),s=oe(r,this._service.monomerLib,{mode:"lenient"}).mol;this._replaceMol(s,`replaceMonomer:${n}->${t}`,"api");let a=g(s,e.id);void 0!==a&&this._events.fire("monomer:replace",{atom:a,oldSymbol:n,newSymbol:t})}hitTest(e,t){this._ensureLive();let i=new Yi(this._mol,this._theme).test({x:e,y:t});return null===i?null:void 0!==i.atom?{atom:i.atom}:void 0!==i.bond?{bond:i.bond}:null}moveAtom(e,t){this._ensureLive();let i=g(this._mol,e);if(void 0===i||i.p.x===t.x&&i.p.y===t.y)return;let n=new qi(this._mol);n.updateAtom(e,{p:{x:t.x,y:t.y}});let{mol:o}=n.commit();this._replaceMol(o,"moveAtom","user")}moveAtoms(e){if(this._ensureLive(),0===e.length)return;let t=new qi(this._mol),i=0;for(let n of e){let e=g(this._mol,n.atomId);void 0!==e&&(e.p.x===n.p.x&&e.p.y===n.p.y||(t.updateAtom(n.atomId,{p:{x:n.p.x,y:n.p.y}}),i+=1))}if(0===i)return;let{mol:n}=t.commit();this._replaceMol(n,"moveAtom","user")}_layoutOptions(){let e={};return void 0!==this._options.bondLength&&(e.bondLength=this._options.bondLength),void 0!==this._options.monomersPerRow&&(e.monomersPerRow=this._options.monomersPerRow),Object.keys(e).length>0?e:void 0}cleanLayout(e){this._ensureLive(),this._resetLastAction();let t=Et(this._mol,this._layoutOptions());this._mol=t,this._history.push({mol:t,label:"cleanLayout"}),this._events.fire("layout:change",{mol:t,strategy:"auto"}),this._events.fire("mol:changed",{mol:t,changedAtomIds:new Set(t.atoms.map(e=>e.id)),changedBondIds:In,reason:"cleanLayout"})}canUndo(){return this._history.canUndo()}canRedo(){return this._history.canRedo()}undo(){this._ensureLive();let e=this._history.undo();null!==e&&this._restoreFromHistory(e.mol,"undo")}redo(){this._ensureLive();let e=this._history.redo();null!==e&&this._restoreFromHistory(e.mol,"redo")}on(e,t){return this._events.on(e,t)}off(e,t){this._events.off(e,t)}fire(e,t){this._events.fire(e,t)}zoom(e,t){if(this._ensureLive(),!Number.isFinite(e)||e<=0)return;let i=this._viewport.scale,n=Math.min(8,Math.max(.2,i*e));if(n===i)return;let o={...this._viewport.offset},r=o;void 0!==t&&(r={x:o.x+(i-n)*t.x,y:o.y+(i-n)*t.y});let s={scale:n,offset:r};this._viewport=s;let a=t??{x:0,y:0};this._events.fire("view:zoom",{scale:n,center:a,previousScale:i}),this._events.fire("view:viewport-change",{viewport:s})}panTo(e){this._ensureLive();let t={...this._viewport.offset},i={scale:this._viewport.scale,offset:{...e}};this._viewport=i,this._events.fire("view:pan",{offset:i.offset,previousOffset:t}),this._events.fire("view:viewport-change",{viewport:i})}getViewport(){return{scale:this._viewport.scale,offset:{...this._viewport.offset}}}fitToContent(e){this._ensureLive();let t=0,i=0,n=0,o=0,r=!1;for(let e of this._mol.atoms)r?(e.p.x<t&&(t=e.p.x),e.p.x>n&&(n=e.p.x),e.p.y<i&&(i=e.p.y),e.p.y>o&&(o=e.p.y)):(t=n=e.p.x,i=o=e.p.y,r=!0);let s=r?{x:t,y:i,width:n-t,height:o-i}:{x:0,y:0,width:0,height:0},a={...this._viewport.offset},l=this._viewport.scale,h={scale:1,offset:{x:0,y:0}};this._viewport=h,1!==l&&this._events.fire("view:zoom",{scale:1,center:{x:0,y:0},previousScale:l}),(0!==a.x||0!==a.y)&&this._events.fire("view:pan",{offset:h.offset,previousOffset:a}),this._events.fire("view:viewport-change",{viewport:h}),this._events.fire("view:fit-to-content",{bbox:s})}setViewOnly(e){this._ensureLive();let t=this._viewOnly;t!==e&&(this._viewOnly=e,this._events.fire("option:change",{key:"viewOnly",oldValue:t,newValue:e}))}setTheme(e){this._ensureLive();let t=this._theme;t!==e&&(this._theme=e,this._events.fire("theme:change",{theme:e,previousTheme:t}))}toSvg(e){this._ensureLive();let t=this.getHelm(),i={};return void 0!==e?.width&&(i.width=e.width),void 0!==e?.height&&(i.height=e.height),this._service.renderToSvg(t,i)}async toPng(e){this._ensureLive();let t=this.getHelm(),i={};return void 0!==e?.width&&(i.width=e.width),void 0!==e?.height&&(i.height=e.height),this._service.renderToPng(t,i)}_getHost(){return this._host}_observerCount(){return this._events.observerCount()}_currentHighlights(){return this._highlights}_currentTheme(){return this._theme}_getView(){return this._view}_getViewport(){return this._viewport}openAtomProps(e){this._ensureLive(),null!==this._host&&(null===this._atomDialog&&(this._atomDialog=new En(this)),this._atomDialog.open(e))}openBondProps(e){this._ensureLive(),null!==this._host&&(null===this._bondDialog&&(this._bondDialog=new Bn(this)),this._bondDialog.open(e))}openFindReplace(){this._ensureLive(),null!==this._host&&(null===this._findReplaceDialog&&(this._findReplaceDialog=new Tn(this)),this._findReplaceDialog.open())}getMode(){return this._mode}setMode(e){this._ensureLive();let t=this._mode;t!==e&&(this._mode=e,this._events.fire("option:change",{key:"mode",oldValue:t,newValue:e}))}getNextAddSymbol(){return this._nextAdd}setNextAddSymbol(e,t){this._ensureLive();let i=this._nextAdd;if(null===e)this._nextAdd=null;else{if(void 0===t)return;this._nextAdd={symbol:e,biotype:t}}this._events.fire("option:change",{key:"nextAdd",oldValue:i,newValue:this._nextAdd})}startPaletteDrag(e,t){this._ensureLive(),null!==this._dnd?this._dnd.startPaletteDrag(e,t):this._events.fire("dnd:start",{source:"palette",symbol:e})}findMonomers(e){this._ensureLive();let t=[];for(let i of this._mol.atoms)i.symbol===e&&t.push(i);return t}replaceMonomers(e,t){let i,n;if(this._ensureLive(),"string"==typeof e){let o=e,r=t;if(i=this.findMonomers(o),0===i.length)return 0;if(o===r)return i.length;n=`${o}->${r}`}else{let o=t,r=new Set,s=[];for(let t of e){if(r.has(t.id))continue;r.add(t.id);let e=g(this._mol,t.id);void 0!==e&&e.symbol!==o&&s.push(e)}if(0===s.length)return 0;i=s,n=`atoms[${s.length}]->${o}`}let o=t,r=new qi(this._mol);for(let e of i)r.updateAtom(e.id,{symbol:o});let{mol:s}=r.commit(),a=oe(s,this._service.monomerLib,{mode:"lenient"}).mol;return this._replaceMol(a,`replaceMonomers:${n}`,"api"),i.length}nudgeSelection(e,t){this._ensureLive();let i=this._selection;if(0===i.atoms.size)return;let n=new qi(this._mol);for(let o of i.atoms){let i=g(this._mol,o);void 0!==i&&n.updateAtom(o,{p:{x:i.p.x+e,y:i.p.y+t}})}let{mol:o}=n.commit();this._replaceMol(o,"nudge","user")}deleteSelection(){this._ensureLive();let e=this._selection;if(0===e.atoms.size&&0===e.bonds.size)return;let t=new qi(this._mol);for(let i of e.atoms)t.removeAtom(i);for(let i of e.bonds)t.removeBond(i);let{mol:i}=t.commit();this._selection=Di.empty(),this._replaceMol(i,"delete-selection","user"),this._events.fire("selection:change",{selection:this._selection,addedAtomIds:In,removedAtomIds:e.atoms,addedBondIds:In,removedBondIds:e.bonds})}appendRnaTriplet(e,t,i){this._ensureLive();let n=Pn(e,t,i),o=function(e,t){if(""===e)return`RNA1{${t}}$$$$V2.0`;let i,n=/(^|\|)(RNA\d+)\{([^}]*)\}/g,o=null;for(;null!==(i=n.exec(e));)o={name:i[2],body:i[3],matchText:i[0]};if(null!==o){let i=""===o.body?"":".",n=`${o.matchText.startsWith("|")?"|":""}${o.name}{${o.body}${i}${t}}`,r=e.lastIndexOf(o.matchText);return e.slice(0,r)+n+e.slice(r+o.matchText.length)}let r,s=new Set,a=/RNA(\d+)\{/g;for(;null!==(r=a.exec(e));)s.add(Number(r[1]));let l=1;for(;s.has(l);)l+=1;let h=`RNA${l}{${t}}`,d=e.indexOf("$");if(d<0)return`${e}|${h}$$$$V2.0`;let c=e.slice(0,d);return`${c}${""===c?"":"|"}${h}${e.slice(d)}`}(this.getHelm(),n);this.setHelm(o)}placeRnaTriplet(e,t,i){this._ensureLive();let n,o=1.6*(this._options.bondLength??28),r=this._mol.atoms;if("add-triplet"===this._lastAction&&null!==this._lastTripletSugarPos)n={x:this._lastTripletSugarPos.x+2*o,y:this._lastTripletSugarPos.y};else if(0===r.length)n={x:0,y:0};else{let e=r[0].p.x,t=r[0].p.y;for(let i of r)i.p.x<e&&(e=i.p.x),i.p.y>t&&(t=i.p.y);n={x:e,y:t+o}}let s={x:n.x+o,y:n.y},a={x:n.x,y:n.y+o},l=new Set;for(let e of this._mol.chains)l.add(e.id);let h=1;for(;l.has(`RNA${h}`);)h+=1;let d=`RNA${h}`,c=new qi(this._mol),u=c.addAtom({p:n,biotype:v,symbol:e,chainId:d,positionInChain:1}),p=c.addAtom({p:s,biotype:x,symbol:i,chainId:d,positionInChain:2}),m=c.addAtom({p:a,biotype:w,symbol:t,chainId:d,positionInChain:0});c.addBond({a1:u,a2:m,kind:"branch",r1:{kind:"numeric",r:3},r2:{kind:"numeric",r:1}}),c.addBond({a1:u,a2:p,kind:"backbone",r1:{kind:"numeric",r:2},r2:{kind:"numeric",r:1}});let{mol:f}=c.commit(),b=oe(this._postProcessTripletMol(f,u,m,d),this._service.monomerLib,{mode:"lenient"}).mol;this._replaceMol(b,"placeRnaTriplet","user"),this._lastAction="add-triplet",this._lastTripletSugarPos=n}_postProcessTripletMol(e,t,i,n){let o=new Map,r=g(e,i),s=g(e,t);if(void 0===r||void 0===s)return e;let a={...s,branchAtom:r};o.set(t,a);let l=e.bonds.map(e=>{let t=o.get(e.a1.id)??e.a1,i=o.get(e.a2.id)??e.a2;return t===e.a1&&i===e.a2?e:{...e,a1:t,a2:i}}),h=new Map;for(let e of l)h.set(e.id,e);let d=e.chains.map(e=>{let t=[];for(let r of e.backboneAtoms)e.id===n&&r.id===i||t.push(o.get(r.id)??r);let r=e.bonds.map(e=>h.get(e.id)??e);return{id:e.id,polymerType:e.polymerType,backboneAtoms:t,bonds:r,...void 0!==e.annotation?{annotation:e.annotation}:{}}}),c={atoms:e.atoms.map(e=>o.get(e.id)??e),bonds:l,chains:d,groups:e.groups,annotations:e.annotations};return c=this._refreshContinuousIdsLocal(c),c}_resetLastAction(){this._lastAction="other",this._lastTripletSugarPos=null}_ensureLive(){if(this._destroyed)throw new Error("HelmEditor: this instance has been destroyed.")}_replaceMol(e,t,i){let n=this._service.serialize(this._mol),o=this._service.serialize(e);this._mol=e,this._history.push({mol:e,label:t}),this._resetLastAction(),this._events.fire("mol:changed",{mol:e,changedAtomIds:new Set(e.atoms.map(e=>e.id)),changedBondIds:new Set(e.bonds.map(e=>e.id)),reason:t}),n!==o&&this._events.fire("helm:changed",{helm:o,mol:e,source:i})}_restoreFromHistory(e,t){let i=this._service.serialize(this._mol),n=this._service.serialize(e);this._mol=e,this._resetLastAction(),this._events.fire("mol:changed",{mol:e,changedAtomIds:new Set(e.atoms.map(e=>e.id)),changedBondIds:new Set(e.bonds.map(e=>e.id)),reason:t}),i!==n&&this._events.fire("helm:changed",{helm:n,mol:e,source:t})}};function $n(e){return e.startsWith("[")&&e.endsWith("]")||1===e.length&&/^[A-Za-z]$/.test(e)?e:`[${e}]`}function Pn(e,t,i){return`${$n(e)}(${$n(t)})${$n(i)}`}var Rn="http://www.w3.org/2000/svg",Hn={sugar:v,base:w,linker:x},Nn={sugar:["r","R"],base:["A"],linker:["p","P"]},Dn={x:70,y:60},Fn={x:140,y:60},On={x:70,y:130},zn=class e{constructor(e,t,i){this.onValueSet=new I,this.onPickModeChange=new I,this._slots=new Map,this._favStar=null,this._pickMode=null,this._destroyed=!1,this._builderRdkitCache=new Map,this._editor=t,this._doc=i?.documentImpl??Xi(e),this._hooks=i?.paletteHooks??null,this._favHooks=i?.favoriteHooks??null,this.element=Qi(this._doc,"div",{class:"hw-rna-builder","data-testid":"rna-builder"});let n=Qi(this._doc,"div",{class:"hw-rna-builder__header"});if(n.appendChild(Qi(this._doc,"div",{class:"hw-rna-builder__title"},["RNA builder"])),null!==this._favHooks){let e=Qi(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"},["☆"]),t=e=>{e.stopPropagation();let t=this.getSelection();""===t.preview||null===this._favHooks||this._favHooks.toggleFavoriteTriplet(t.sugar,t.base,t.linker)};e.addEventListener("click",t),e.addEventListener("keydown",e=>{let i=e;("Enter"===i.key||" "===i.key)&&t(e)}),this._favStar=e,n.appendChild(e)}this.element.appendChild(n),this._hintEl=Qi(this._doc,"div",{class:"hw-rna-builder__hint","data-testid":"rna-builder-hint",hidden:!0}),this.element.appendChild(this._hintEl);let o=this._buildSvg();this.element.appendChild(o),this._preview=Qi(this._doc,"div",{class:"hw-rna-builder__preview","data-testid":"rna-builder-preview"}),this.element.appendChild(this._preview),this._addBtn=Qi(this._doc,"button",{class:"hw-rna-builder__add",type:"button","data-testid":"rna-builder-add-btn"},["Add triplet"]),this._addBtn.addEventListener("click",()=>this._onAddClicked()),this.element.appendChild(this._addBtn),e.appendChild(this.element);let r=t.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),s=t.on("theme:change",()=>{this._destroyed||this._repaintSlotColors()});this._libUnsub=()=>{try{r()}catch{}try{s()}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}getSelection(){let e=this._slots.get("sugar")?.value??"",t=this._slots.get("base")?.value??"",i=this._slots.get("linker")?.value??"";return{sugar:e,base:t,linker:i,preview:""!==e&&""!==t&&""!==i?Pn(e,t,i):""}}setField(e,t){let i=this._slots.get(e);void 0!==i&&(i.value=t,this._setLabelText(i.labelEl,t),this._repaintSlot(i),this._updatePreview(),this.onValueSet.next({field:e,symbol:t}))}startPickMode(e){this._pickMode!==e?(null!==this._pickMode&&this._setSlotPressed(this._pickMode,!1),this._pickMode=e,this._setSlotPressed(e,!0),this._setHintActive(e),this.onPickModeChange.next({field:e}),null!==this._hooks&&this._hooks.beginBiotypeFilter(Hn[e],t=>{this.setField(e,t),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 e=this._doc.createElementNS(Rn,"svg");e.setAttribute("class","hw-rna-builder__triplet"),e.setAttribute("viewBox","0 0 200 180"),e.setAttribute("data-testid","rna-builder-triplet-svg"),e.setAttribute("role","group"),e.setAttribute("aria-label","Triplet preview");let t=this._doc.createElementNS(Rn,"line");t.setAttribute("class","hw-rna-builder__bond"),t.setAttribute("x1",String(Dn.x+18)),t.setAttribute("y1",String(Dn.y)),t.setAttribute("x2",String(Fn.x-18)),t.setAttribute("y2",String(Fn.y)),e.appendChild(t);let i=this._doc.createElementNS(Rn,"line");i.setAttribute("class","hw-rna-builder__bond"),i.setAttribute("x1",String(Dn.x)),i.setAttribute("y1",String(Dn.y+18)),i.setAttribute("x2",String(On.x)),i.setAttribute("y2",String(On.y-22)),e.appendChild(i);let n=this._doc.createElementNS(Rn,"rect");n.setAttribute("class","hw-rna-builder__slot-shape"),n.setAttribute("x",String(-18)),n.setAttribute("y",String(-18)),n.setAttribute("width",String(36)),n.setAttribute("height",String(36)),n.setAttribute("rx","8"),n.setAttribute("ry","8");let o=this._buildSlot("sugar","Pick sugar (backbone)",Dn,n),r=this._doc.createElementNS(Rn,"circle");r.setAttribute("class","hw-rna-builder__slot-shape"),r.setAttribute("cx","0"),r.setAttribute("cy","0"),r.setAttribute("r",String(18));let s=this._buildSlot("linker","Pick linker",Fn,r),a=this._doc.createElementNS(Rn,"path");a.setAttribute("class","hw-rna-builder__slot-shape"),a.setAttribute("d","M -22 0 L 0 -22 L 22 0 L 0 22 Z");let l=this._buildSlot("base","Pick base",On,a);return e.appendChild(s.groupEl),e.appendChild(o.groupEl),e.appendChild(l.groupEl),this._slots.set("sugar",o),this._slots.set("linker",s),this._slots.set("base",l),e}_buildSlot(e,t,i,n){let o=this._doc.createElementNS(Rn,"g");o.setAttribute("class","hw-rna-builder__slot"),o.setAttribute("data-slot",e),o.setAttribute("data-testid",`rna-builder-slot-${e}`),o.setAttribute("role","button"),o.setAttribute("tabindex","0"),o.setAttribute("aria-label",t),o.setAttribute("aria-pressed","false"),o.setAttribute("transform",`translate(${i.x} ${i.y})`),o.appendChild(n);let r=this._doc.createElementNS(Rn,"text");r.setAttribute("class","hw-rna-builder__slot-label"),r.setAttribute("data-testid",`rna-builder-${e}-value`),r.setAttribute("x","0"),r.setAttribute("y","0"),r.setAttribute("text-anchor","middle"),r.setAttribute("dominant-baseline","central"),o.appendChild(r);let s=t=>{t.stopPropagation(),this.startPickMode(e)};return o.addEventListener("click",s),o.addEventListener("keydown",e=>{let t=e;("Enter"===t.key||" "===t.key)&&s(e)}),o.addEventListener("mouseenter",t=>this._showSlotTooltip(e,t)),o.addEventListener("mouseleave",()=>this._hideSlotTooltip()),o.addEventListener("focus",()=>this._showSlotTooltip(e,null)),o.addEventListener("blur",()=>this._hideSlotTooltip()),{id:e,biotype:Hn[e],groupEl:o,shapeEl:n,labelEl:r,value:""}}_setLabelText(e,t){let i=[];for(let t=e.firstChild;null!==t;t=t.nextSibling)"title"===t.nodeName||"TITLE"===t.nodeName||i.push(t);for(let t of i)e.removeChild(t);let n=function(e){let t=e.length;return t<=2?16:t<=4?11:t<=7?8:t<=10?6:5}(t);e.setAttribute("font-size",String(n)),e.setAttribute("text-anchor","middle"),e.setAttribute("dominant-baseline","central");let o=t.length>10?`${t.slice(0,9)}…`:t;e.appendChild(this._doc.createTextNode(o));let r=e.parentNode;if(null!==r){let e=null;for(let t=r.firstChild;null!==t;t=t.nextSibling)if("title"===t.nodeName||"TITLE"===t.nodeName){e=t;break}for(null===e&&(e=this._doc.createElementNS(Rn,"title"),r.insertBefore(e,r.firstChild));null!==e.firstChild;)e.removeChild(e.firstChild);e.appendChild(this._doc.createTextNode(t))}}_repaintSlotColors(){for(let e of this._slots.values())this._repaintSlot(e)}_repaintSlot(e){let t=this._editor.getService().monomerLib,i=this._theme(),n=""===e.value?null:function(e,t,i){return e.getMonomerSet(t).get(i)??null}(t,e.biotype,e.value),o=te(n,e.biotype,i.colorTheme);e.shapeEl.style.fill=o.background,e.shapeEl.style.stroke=o.line,e.labelEl.style.fill=o.text}_populateDefaults(){let e=this._editor.getService().monomerLib;for(let[t,i]of this._slots.entries()){let n=qn(e,i.biotype),o=jn(n,Nn[t]),r=""!==i.value&&n.some(e=>e.symbol===i.value)?i.value:o??n[0]?.symbol??"";i.value=r,this._setLabelText(i.labelEl,r)}}_updatePreview(){let e=this.getSelection();for(;null!==this._preview.firstChild;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(""===e.preview?"-":e.preview)),this._updateFavStar(e)}_updateFavStar(e){if(null===this._favStar||null===this._favHooks)return;let t=""!==e.preview,i=t&&this._favHooks.isFavoriteTriplet(e.sugar,e.base,e.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"),t?this._favStar.removeAttribute("aria-disabled"):this._favStar.setAttribute("aria-disabled","true");let n="hw-rna-builder__fav"+(i?" hw-rna-builder__fav--active":"")+(t?"":" hw-rna-builder__fav--disabled");this._favStar.setAttribute("class",n)}_onAddClicked(){let e=this.getSelection();""!==e.preview&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)}_exitPickMode(){if(null===this._pickMode)return;let e=this._pickMode;this._setSlotPressed(e,!1),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null})}_setHintActive(e){let t=this._hintEl;for(;null!==t.firstChild;)t.removeChild(t.firstChild);if(null===e)return void t.setAttribute("hidden","");t.removeAttribute("hidden");let i="sugar"===e?"sugar":"base"===e?"base":"linker";t.appendChild(this._doc.createTextNode(`Pick ${i} from palette`))}_setSlotPressed(e,t){let i=this._slots.get(e);if(void 0===i)return;i.groupEl.setAttribute("aria-pressed",t?"true":"false");let n=(i.groupEl.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-rna-builder__slot--active"!==e).join(" ");i.groupEl.setAttribute("class",t?`${n} hw-rna-builder__slot--active`:n)}_theme(){let e=this._editor;return"function"==typeof e._currentTheme?e._currentTheme():this._editor.getService().theme}_rdkit(){let e=this._editor.getService().options?.rdkitModule;return e??null}_builderRdkitSvgFor(t){if(null===t)return null;let i=t.smiles;if(void 0===i||""===i)return null;let n=this._rdkit();if(null===n)return null;let o=`${t.polymerType}:${t.symbol}`;if(this._builderRdkitCache.has(o))return this._builderRdkitCache.get(o)??null;let r=Zi(n,i,220,140);if(this._builderRdkitCache.size>=e._BUILDER_RDKIT_CACHE_LIMIT){let e=this._builderRdkitCache.keys().next().value;void 0!==e&&this._builderRdkitCache.delete(e)}return this._builderRdkitCache.set(o,r),r}_slotHint(e){switch(e){case"sugar":return"Click to choose a different sugar";case"base":return"Click to choose a different base";case"linker":return"Click to choose a different linker"}}_slotTitle(e,t){let i=""===t?"?":t;switch(e){case"sugar":return`Sugar: ${i}`;case"base":return`Base: ${i}`;case"linker":return`Linker: ${i}`}}_showSlotTooltip(e,t){let i=this._slots.get(e);if(void 0===i)return;let n=this._editor.getService().monomerLib.getMonomerSet(i.biotype),o=""===i.value?null:n.get(i.value)??null,r=Ji(this._doc,"builder-tooltip","hw-builder-tooltip");en(this._doc,r,{symbol:this._slotTitle(e,i.value),name:o?.name??"",rdkitSvg:this._builderRdkitSvgFor(o),rdkitTestid:"builder-tooltip-rdkit-svg",hint:this._slotHint(e)});let s=t;if(null!==s&&"number"==typeof s.clientX&&"number"==typeof s.clientY)tn(r,s.clientX,s.clientY);else{let e=i.groupEl,t="function"==typeof e.getBoundingClientRect?e.getBoundingClientRect():null;null!==t?tn(r,t.left+t.width/2,t.top+t.height/2):tn(r,0,0)}}_hideSlotTooltip(){nn(this._doc.body.querySelector('[data-testid="builder-tooltip"]'))}};zn._BUILDER_RDKIT_CACHE_LIMIT=256;var Gn=zn;function qn(e,t){let i=e.getMonomerSet(t),n=[];for(let e of i.values())n.push(e);return n.sort((e,t)=>e.symbol.localeCompare(t.symbol)),n}function jn(e,t){let i=new Set;for(let t of e)i.add(t.symbol);for(let e of t)if(i.has(e))return e;return null}var Yn="Favorites",Vn={[Yn]:"★ Favorites",[B.PEPTIDE]:"Peptides",[B.RNA]:"RNA",[B.CHEM]:"CHEM",[B.BLOB]:"BLOB",G:"G"},Wn=[Yn,B.PEPTIDE,B.RNA,B.CHEM,B.BLOB,"G"],Un="hwe:palette:favorites",Kn="hwe:palette:active-tab";function Xn(e){return`${e.sugar}|${e.base}|${e.linker}`}var Qn=class e{constructor(e,t,i){this.favoritesChanged=new I,this._nextAddUnsub=()=>{},this._favorites=new Set,this._favoriteTriplets=[],this._pendingRnaSelection=null,this._visibleTabs=[Yn],this._activeTab=Yn,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=t,this._doc=i?.documentImpl??Xi(e),this._opts={documentImpl:this._doc,groupByNaturalAnalog:i?.groupByNaturalAnalog??!0,allowFavorites:i?.allowFavorites??!0},this._loadFavorites(),this._activeTab=this._resolveInitialTab(i?.initialTab),this.element=Qi(this._doc,"div",{class:"hw-palette","data-testid":"palette"}),e.appendChild(this.element),this._render(),this._libUnsub=t.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),this._themeUnsub=t.on("theme:change",()=>{this._destroyed||this.refresh()}),this._nextAddUnsub=t.on("option:change",e=>{this._destroyed||"nextAdd"===e.key&&this._updatePrimedClasses()})}refresh(){this._render()}setFilter(e){this._filter=e.trim().toLowerCase(),null!==this._searchInput&&this._searchInput.value!==e&&(this._searchInput.value=e),this._applyFilter()}setActiveTab(e){this._visibleTabs.includes(e)&&(this._activeTab=e,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter())}getActiveTab(){return this._activeTab}getFavorites(){let e=this._editor.getService().monomerLib,t=[];for(let i of this._favorites)null!==this._findMonomer(e,i)&&t.push(i);return t}setFavorite(e,t){t!==this._favorites.has(e)&&(t?this._favorites.add(e):this._favorites.delete(e),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(e=>({...e}))}isFavoriteTriplet(e,t,i){let n=Xn({sugar:e,base:t,linker:i});return this._favoriteTriplets.some(e=>Xn(e)===n)}setFavoriteTriplet(e,t,i,n){let o=Xn({sugar:e,base:t,linker:i}),r=this._favoriteTriplets.findIndex(e=>Xn(e)===o);n!==r>=0&&(n?this._favoriteTriplets.push({sugar:e,base:t,linker:i}):this._favoriteTriplets.splice(r,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}_hidePaletteTooltips(){let e=this._doc.body;nn(e.querySelector('[data-testid="palette-tooltip"]')),nn(e.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 e=this._pickCanceller;this._teardownPickMode(),e?.()}_buildPaletteFilterHooks(){return{beginBiotypeFilter:(e,t,i)=>{null!==this._activeBiotypeFilter&&this._teardownPickMode(),this._activeBiotypeFilter=e,this._pickResolver=t,this._pickCanceller=i,this._applyFilter();let n=e=>{"Escape"===e.key&&this.cancelBiotypeFilter()};this._pickEscapeListener=n,this._doc.defaultView?.addEventListener("keydown",n);let o=e=>{if(null===this._activeBiotypeFilter)return;let t=e.target;if(null==t)return;let i=this._activeBiotypeFilter,n=t;for(;null!==n;){let e=void 0===n.getAttribute?null:n.getAttribute("class");if(null!==e){let t=e.split(/\s+/);if(t.includes("hw-palette__tile")){if((n.getAttribute("data-biotype")??"")===i)return;break}if(t.includes("hw-rna-builder__slot")){if(this._isInsideOwnPalette(n))return;break}}n=n.parentElement}this.cancelBiotypeFilter()};this._pickOutsideClickListener=o,this._doc.addEventListener("mousedown",o,!0)},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let e=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`);if(null===e)return;let t=e;try{if("function"==typeof t.scrollTo)return void t.scrollTo({top:0,behavior:"smooth"})}catch{}"number"==typeof t.scrollTop&&(t.scrollTop=0)}_isInsideOwnPalette(e){let t=e;for(;null!==t;){if(t===this.element)return!0;t=t.parentElement}return!1}_teardownPickMode(){null!==this._activeBiotypeFilter&&(this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,null!==this._pickEscapeListener&&(this._doc.defaultView?.removeEventListener("keydown",this._pickEscapeListener),this._pickEscapeListener=null),null!==this._pickOutsideClickListener&&(this._doc.removeEventListener("mousedown",this._pickOutsideClickListener,!0),this._pickOutsideClickListener=null),this._applyFilter())}_render(){for(null!==this._rnaBuilder&&(this._pendingRnaSelection=this._rnaBuilder.getSelection(),this._rnaBuilder.destroy(),this._rnaBuilder=null);null!==this.element.firstChild;)this.element.removeChild(this.element.firstChild);let e=this._doc.createElement("input");e.setAttribute("type","search"),e.setAttribute("class","hw-palette__search"),e.setAttribute("placeholder","Search monomers..."),e.setAttribute("data-testid","palette-search"),""!==this._filter&&(e.value=this._filter),e.addEventListener("input",()=>this.setFilter(e.value)),this._searchInput=e,this.element.appendChild(e),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=Yn);let t=Qi(this._doc,"div",{class:"hw-palette__tabs",role:"tablist","data-testid":"palette-tabs"});for(let e of this._visibleTabs){let i=e===this._activeTab,n=Qi(this._doc,"button",{class:"hw-palette__tab",type:"button",role:"tab","aria-controls":`hw-palette-pane-${e}`,"aria-selected":i?"true":"false","data-testid":`palette-tab-${e}`,"data-tab":e,title:Vn[e]},[Vn[e]]);n.addEventListener("click",()=>this.setActiveTab(e)),t.appendChild(n)}this.element.appendChild(t);let i=Qi(this._doc,"div",{class:"hw-palette__panes"}),n=this._theme(),o=this._editor.getService().monomerLib;for(let e of this._visibleTabs){let t=e===this._activeTab,r=Qi(this._doc,"div",{class:"hw-palette__pane",id:`hw-palette-pane-${e}`,role:"tabpanel","data-testid":`palette-pane-${e}`,"data-tab":e,hidden:!t});e===Yn?this._buildFavoritesPane(r,o,n):this._buildPolymerPane(r,e,o,n),i.appendChild(r)}this.element.appendChild(i),this._applyFilter()}_computeVisibleTabs(){let e=this._editor.getService().monomerLib,t=new Set;for(let i of e.getPolymerTypes())t.add(i);let i=[];i.push(Yn);for(let e of Wn)e!==Yn&&t.has(e)&&i.push(e);return i}_buildFavoritesPane(e,t,i){let n=this._resolveFavoriteMonomers(t),o=this._favoriteTriplets;if(0===n.length&&0===o.length){let t=Qi(this._doc,"div",{class:"hw-palette__placeholder","data-testid":"palette-favorites-empty"},["No favorites yet — click the ☆ on any tile to add one."]);return void e.appendChild(t)}for(let[t,i]of this._groupByPolymerAndType(n))e.appendChild(this._renderGroup(t,i));o.length>0&&e.appendChild(this._renderTripletGroup("RNA · Triplets",o,t))}_groupByPolymerAndType(e){let t=new Map;for(let i of e){let e=i.polymerType,n=i.monomerType??"Undefined",o=`${e}|${n}`,r=t.get(o);void 0===r&&(r={pt:e,mt:n,list:[]},t.set(o,r)),r.list.push(i)}let i=e=>{let t=Wn.indexOf(e);return t<0?99:t},n={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(t.values()).sort((e,t)=>i(e.pt)-i(t.pt)||(n[e.mt]??9)-(n[t.mt]??9)||e.mt.localeCompare(t.mt)).map(e=>[`${this._polymerLabel(e.pt)} · ${e.mt}`,e.list])}_polymerLabel(e){return Vn[e]??e}_renderTripletGroup(e,t,i){let n=Qi(this._doc,"div",{class:"hw-palette__group","data-natural-analog":e}),o=Qi(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${e}`},[e]),r=Qi(this._doc,"div",{class:"hw-triplet-chips","data-testid":"palette-triplet-favorites"});for(let e of t)r.appendChild(this._renderTripletChip(e,i));return n.appendChild(o),n.appendChild(r),n}_renderTripletChip(e,t){let i=Pn(e.sugar,e.base,e.linker),n=t.getMonomerSet(w).get(e.base)??null,o=te(n,w,this._theme().colorTheme),r=this.isFavoriteTriplet(e.sugar,e.base,e.linker),s=void 0!==n?.name&&""!==n.name?`${i} — ${n.name}`:i,{root:a}=function(e,t){let i=!1!==t.showStar,n=Qi(e,"span",{class:"hw-triplet-chip__star"},[t.favorite?"★":"☆"]),o=Qi(e,"span",{class:"hw-triplet-chip__label"},[t.label]),r=["hw-triplet-chip"];t.favorite&&r.push("hw-triplet-chip--favorite");let s=i?[n,o]:[o];return{root:Qi(e,"div",{class:r.join(" "),role:"button",tabindex:"0","aria-label":t.title,"data-sugar":t.sugar,"data-base":t.base,"data-linker":t.linker,"data-triplet":t.label,"data-testid":`palette-triplet-${t.label}`,title:t.title,style:`background:${t.background};color:${t.textColor};`},s),star:n}}(this._doc,{sugar:e.sugar,base:e.base,linker:e.linker,label:i,title:s,background:O(o.background),textColor:o.text,favorite:r,showStar:this._opts.allowFavorites});return this._wireTripletChip(a,e),a}_wireTripletChip(e,t){e.addEventListener("mouseenter",e=>{let i=e,n=Ji(this._doc,"palette-triplet-tooltip","hw-palette-tooltip hw-triplet-tooltip");(function(e,t,i){for(;null!==t.firstChild;)t.removeChild(t.firstChild);t.appendChild(Qi(e,"div",{class:"hw-tooltip__symbol"},[i.title]));let n=Qi(e,"div",{class:"hw-tooltip__triplet"});for(let t of i.parts){let o=Qi(e,"div",{class:"hw-tooltip__triplet-part"});if(o.appendChild(Qi(e,"div",{class:"hw-tooltip__triplet-role"},[`${t.role}: ${t.symbol}`])),void 0!==t.name&&""!==t.name&&t.name!==t.symbol&&o.appendChild(Qi(e,"div",{class:"hw-tooltip__name"},[t.name])),void 0!==t.rdkitSvg&&null!==t.rdkitSvg&&""!==t.rdkitSvg){let n={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(n["data-testid"]=i.rdkitTestid);let r=Qi(e,"div",n);r.innerHTML=t.rdkitSvg,o.appendChild(r)}n.appendChild(o)}t.appendChild(n),void 0!==i.hint&&""!==i.hint&&t.appendChild(Qi(e,"div",{class:"hw-tooltip__hint"},[i.hint]))})(this._doc,n,{title:Pn(t.sugar,t.base,t.linker),parts:this._tripletTooltipParts(t),hint:"Click to add this triplet",rdkitTestid:"palette-triplet-tooltip-rdkit-svg"}),tn(n,"number"==typeof i.clientX?i.clientX:0,"number"==typeof i.clientY?i.clientY:0)}),e.addEventListener("mouseleave",()=>{nn(this._doc.body.querySelector('[data-testid="palette-triplet-tooltip"]'))}),e.addEventListener("click",e=>{let i=e.target;if(this._opts.allowFavorites&&!0===i?.classList?.contains("hw-triplet-chip__star"))return this.setFavoriteTriplet(t.sugar,t.base,t.linker,!this.isFavoriteTriplet(t.sugar,t.base,t.linker)),void e.stopPropagation();this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)}),e.addEventListener("keydown",e=>{let i=e;("Enter"===i.key||" "===i.key)&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)})}_buildRnaDefaultChips(t){let i=this._pickSymbol(t.getMonomerSet(v),["r","R"]),n=this._pickSymbol(t.getMonomerSet(x),["p","P"]),o=t.getMonomerSet(w);if(null===i||null===n)return null;let r=e._DEFAULT_TRIPLET_BASES.filter(e=>o.has(e));if(0===r.length)return null;let s=Qi(this._doc,"div",{class:"hw-triplet-chips hw-triplet-chips--defaults","data-testid":"rna-default-triplets"});for(let e of r)s.appendChild(this._renderTripletChip({sugar:i,base:e,linker:n},t));return s}_tripletTooltipParts(e){let t=this._editor.getService().monomerLib,i=(e,i,n)=>{let o=t.getMonomerSet(i).get(n)??null;return{role:e,symbol:n,...void 0!==o?.name?{name:o.name}:{},rdkitSvg:null===o?null:this._paletteRdkitSvg(o)}};return[i("Sugar",v,e.sugar),i("Base",w,e.base),i("Linker",x,e.linker)]}_pickSymbol(e,t){for(let i of t)if(e.has(i))return i;let i=e.keys().next();return!0===i.done?null:i.value}_restoreRnaSelection(){let e=this._pendingRnaSelection;if(this._pendingRnaSelection=null,null===e||null===this._rnaBuilder)return;let t=this._editor.getService().monomerLib;""!==e.sugar&&t.getMonomerSet(v).has(e.sugar)&&this._rnaBuilder.setField("sugar",e.sugar),""!==e.base&&t.getMonomerSet(w).has(e.base)&&this._rnaBuilder.setField("base",e.base),""!==e.linker&&t.getMonomerSet(x).has(e.linker)&&this._rnaBuilder.setField("linker",e.linker)}_resolveFavoriteMonomers(e){let t=[];for(let i of this._favorites){let n=this._findMonomer(e,i);null!==n&&t.push(n)}return t}_findMonomer(e,t){for(let i of e.getPolymerTypes()){let n=e.getMonomer(i,t);if(null!==n)return n}return null}_buildPolymerPane(e,t,i,n){let o=t,r=this._monomersForPolymer(o,i);if(0===r.length)return;if(o===B.RNA){this._rnaBuilder=new Gn(e,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(e,t,i)=>this.isFavoriteTriplet(e,t,i),toggleFavoriteTriplet:(e,t,i)=>this.setFavoriteTriplet(e,t,i,!this.isFavoriteTriplet(e,t,i))}:null}),this._restoreRnaSelection();let t=this._buildRnaDefaultChips(i);null!==t&&e.appendChild(t);let n=this._groupRna(r);for(let[t,i]of n)0!==i.length&&e.appendChild(this._renderGroup(t,i));return}if(o===B.PEPTIDE&&this._opts.groupByNaturalAnalog){let t=this._groupByAnalog(r);for(let[i,n]of t){let t=""===i?"Other":i;e.appendChild(this._renderGroup(t,n))}return}let s=Qi(this._doc,"div",{class:"hw-palette__group-tiles"}),a=this._editor.getNextAddSymbol(),l=this._sortByColor(r);for(let e of l){let t=this._biotype(e,o);s.appendChild(this._renderTile(e,t,a))}e.appendChild(s)}_renderGroup(e,t){let i=Qi(this._doc,"div",{class:"hw-palette__group","data-natural-analog":e}),n=Qi(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${e}`},[e]),o=Qi(this._doc,"div",{class:"hw-palette__group-tiles"}),r=this._editor.getNextAddSymbol(),s=this._sortByColor(t);for(let e of s){let t=this._biotype(e,e.polymerType);o.appendChild(this._renderTile(e,t,r))}return i.appendChild(n),i.appendChild(o),i}_sortByColor(e){let t=this._theme(),i=e.map((e,i)=>{let n=function(e){let t=P(e);if(null===t)return{h:0,s:0,l:0};let[i,n,o]=N(t[0],t[1],t[2]);return{h:i,s:n,l:o}}(te(e,this._biotype(e,e.polymerType),t.colorTheme).background),o=0===n.s?1:0;return{m:e,idx:i,h:n.h,s:n.s,l:n.l,isGrey:o}});return i.sort((e,t)=>e.isGrey!==t.isGrey?e.isGrey-t.isGrey:e.h!==t.h?e.h-t.h:e.s!==t.s?e.s-t.s:e.l!==t.l?e.l-t.l:e.idx-t.idx),i.map(e=>e.m)}_monomersForPolymer(e,t){let i=t.getMonomerSymbolsByType(e),n=[];for(let o of i){let i=t.getMonomer(e,o);null!==i&&n.push(i)}return n.sort((e,t)=>e.symbol.localeCompare(t.symbol)),n}_groupByAnalog(e){let t=new Map;for(let i of e){let e=i.naturalAnalog??"",n=t.get(e);void 0===n&&(n=[],t.set(e,n)),n.push(i)}let i=[],n=Array.from(t.keys()).sort((e,t)=>""===e&&""!==t?1:""===t&&""!==e?-1:e.localeCompare(t));for(let e of n)i.push([e,t.get(e)]);return new Map(i)}_groupRna(e){let t=[],i=[],n=[],o=[];for(let r of e){let e=ne(r);e===v?t.push(r):e===w?i.push(r):e===x?n.push(r):o.push(r)}let r=new Map;return r.set("Backbones",t),r.set("Bases",i),r.set("Linkers",n),o.length>0&&r.set("Other",o),r}_renderTile(e,t,i){let n=this._favorites.has(e.symbol),o=null!==i&&i.symbol===e.symbol&&i.biotype===t,{root:r,star:s}=function(e,t){let i=te(t.monomer,t.biotype,t.theme.colorTheme),n=O(i.background),o=i.text,r=function(e,t){let i=z(e),n=z(t);return(Math.max(i,n)+.05)/(Math.min(i,n)+.05)}(o,n)<5,s=t.monomer.symbol,a=function(e){return e<=3?14:e<=6?11:e<=9?9:8}(s.length),l=`font-size:${a}px;${s.length>=10?"line-height:1.1;letter-spacing:-0.02em;":""}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:80px;display:inline-block;`,h=Qi(e,"span",{class:"hw-palette__star"},[t.favorite?"★":"☆"]),d=Qi(e,"span",{class:"hw-palette__label",style:l},[s]),c=["hw-palette__tile"];t.primed&&c.push("hw-palette__tile--primed"),t.favorite&&c.push("hw-palette__tile--favorite"),r&&c.push("hw-palette__tile--low-contrast");let u=void 0!==t.monomer.name?`${s} — ${t.monomer.name}`:s,p=`background:${n};color:${o};width:100%;min-width:48px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return{root:Qi(e,"div",{class:c.join(" "),draggable:"true",role:"button","aria-pressed":t.primed?"true":"false","aria-label":u,"data-symbol":s,"data-biotype":t.biotype,"data-bg":n,"data-raw-bg":i.background,"data-testid":`palette-tile-${s}`,title:u,style:p},[h,d]),star:h}}(this._doc,{monomer:e,biotype:t,theme:this._theme(),favorite:n,primed:o});return this._wireTile(r,s,e,t),r}_rdkit(){let e=this._editor.getService().options?.rdkitModule;return e??null}_paletteRdkitSvg(t){let i=t.smiles;if(void 0===i||""===i)return null;let n=this._rdkit();if(null===n)return null;let o=`${t.polymerType}:${t.symbol}`;if(this._paletteRdkitCache.has(o))return this._paletteRdkitCache.get(o)??null;let r=Zi(n,i,220,140);if(this._paletteRdkitCache.size>=e._PALETTE_RDKIT_CACHE_LIMIT){let e=this._paletteRdkitCache.keys().next().value;void 0!==e&&this._paletteRdkitCache.delete(e)}return this._paletteRdkitCache.set(o,r),r}_wireTile(e,t,i,n){e.addEventListener("mouseenter",e=>{let t=e,n=Ji(this._doc,"palette-tooltip","hw-palette-tooltip");en(this._doc,n,{symbol:i.symbol,name:i.name??"",rdkitSvg:this._paletteRdkitSvg(i),rdkitTestid:"palette-tooltip-rdkit-svg"}),tn(n,"number"==typeof t.clientX?t.clientX:0,"number"==typeof t.clientY?t.clientY:0)}),e.addEventListener("mouseleave",()=>{nn(this._doc.body.querySelector('[data-testid="palette-tooltip"]'))}),e.addEventListener("click",e=>{let t=e.target;if(this._opts.allowFavorites&&void 0!==t&&!0===t?.classList?.contains("hw-palette__star"))return this.setFavorite(i.symbol,!this._favorites.has(i.symbol)),void e.stopPropagation();if(null!==this._activeBiotypeFilter&&this._activeBiotypeFilter===n){let t=this._pickResolver;return this._teardownPickMode(),t?.(i.symbol),this._scrollActivePaneToTop(),void e.stopPropagation()}let o=this._editor.getSelection();if(o.atoms.size>0){let 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").toLowerCase(),s=(""===e||r.indexOf(e)>=0)&&null===t;n.style.display=s?"":"none"}let r=(i??this.element).querySelectorAll(".hw-palette__group");for(let e=0;e<r.length;e++){let t=r[e],i=t.querySelectorAll(".hw-palette__tile, .hw-triplet-chip"),n=!1;for(let e=0;e<i.length;e++)if("none"!==i[e].style.display){n=!0;break}n?(t.removeAttribute("hidden"),t.removeAttribute("data-section-empty")):(t.setAttribute("hidden",""),t.setAttribute("data-section-empty","true"))}}_updatePrimedClasses(){let e=this._editor.getNextAddSymbol(),t=this.element.querySelectorAll(".hw-palette__tile");for(let i=0;i<t.length;i++){let n=t[i],o=n.getAttribute("data-symbol")??"",r=n.getAttribute("data-biotype")??"",s=null!==e&&e.symbol===o&&e.biotype===r,a=(n.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-palette__tile--primed"!==e).join(" ");n.setAttribute("class",s?`${a} hw-palette__tile--primed`:a),n.setAttribute("aria-pressed",s?"true":"false")}}_applyActiveTabClasses(){let 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undone action",eraser:"Eraser — click an atom or bond to delete it",select:"Select mode (default)",hbond:"H-Bond mode — drag between two RNA bases to add a Watson-Crick pair","zoom-in":"Zoom in","zoom-out":"Zoom out",fit:"Fit to content — reset zoom and pan",move:"Move/Pan mode — drag the canvas to scroll",clean:"Clean layout — re-run automatic layout",find:"Find / Replace monomer",theme:"Toggle dark / light theme"},io=[{id:"new",label:"New",icon:"New"},{id:"open",label:"Open",icon:"Open"},{id:"save",label:"Save",icon:"Save"},{id:"undo",label:"Undo",icon:"↺",shortcut:"Ctrl+Z",separator:!0},{id:"redo",label:"Redo",icon:"↻",shortcut:"Ctrl+Y"},{id:"eraser",label:"Eraser",icon:"Eraser",separator:!0},{id:"select",label:"Select",icon:"Select"},{id:"hbond",label:"H-Bond",icon:"H-Bond"},{id:"zoom-in",label:"Zoom In",icon:"+",shortcut:"Ctrl++",separator:!0},{id:"zoom-out",label:"Zoom Out",icon:"−",shortcut:"Ctrl+−"},{id:"fit",label:"Fit",icon:"Fit",shortcut:"0"},{id:"move",label:"Move",icon:"Move"},{id:"clean",label:"Clean",icon:"Clean",separator:!0},{id:"find",label:"Find",icon:"Find",shortcut:"Ctrl+F"},{id:"theme",label:"Theme",icon:"Theme",separator:!0}],no=class{constructor(e,t,i){this._buttons=new Map,this._unsubs=[],this._destroyed=!1,this._editor=t,this._doc=i?.documentImpl??Xi(e);let n=i?.buttons??io;this.element=Qi(this._doc,"div",{class:"hw-toolbar","data-testid":"toolbar"}),e.appendChild(this.element);for(let e of n){if(!0===e.separator){let e=Qi(this._doc,"span",{class:"hw-toolbar__separator"});this.element.appendChild(e)}let t=this._buildButton(e);this.element.appendChild(t),this._buttons.set(e.id,t)}let o=()=>this._refreshHistoryState();this._unsubs.push(t.on("mol:changed",o)),this._unsubs.push(t.on("helm:changed",o)),o(),this._reflectMode(),this._unsubs.push(t.on("option:change",e=>{"mode"===e.key&&this._reflectMode()}))}setButtonEnabled(e,t){let i=this._buttons.get(e);void 0!==i&&(t?i.removeAttribute("disabled"):i.setAttribute("disabled",""))}destroy(){if(!this._destroyed){this._destroyed=!0,this._hideTip();for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_buildButton(e){let t=this._doc.createElement("button");t.setAttribute("class","hw-toolbar__btn"),t.setAttribute("type","button"),t.setAttribute("data-action",e.id),t.setAttribute("data-testid",`toolbar-${e.id}`);let i=to[e.id]??e.label,n=void 0!==e.shortcut?`${i} (${e.shortcut})`:i;t.setAttribute("data-tooltip",n),t.setAttribute("aria-label",i),t.addEventListener("mouseenter",e=>{let t=e;this._showTip(n,"number"==typeof t.clientX?t.clientX:0,"number"==typeof t.clientY?t.clientY:0)}),t.addEventListener("mouseleave",()=>this._hideTip()),t.addEventListener("click",()=>this._hideTip());let o=eo[e.id];if(void 0!==o){let e=this._doc.createElement("span");e.setAttribute("class","hw-toolbar__btn-icon"),e.setAttribute("aria-hidden","true"),e.innerHTML=o,t.appendChild(e)}else{let i=e.icon??e.label;t.appendChild(this._doc.createTextNode(i))}return t.addEventListener("click",()=>this._invoke(e.id)),t}_showTip(e,t,i){let n=Ji(this._doc,"toolbar-tooltip","hw-toolbar-tooltip");for(;null!==n.firstChild;)n.removeChild(n.firstChild);n.appendChild(this._doc.createTextNode(e)),tn(n,t,i)}_hideTip(){nn(this._doc.body.querySelector('[data-testid="toolbar-tooltip"]'))}_invoke(e){let t=!1;this._editor.fire("key:command",{command:e,preventDefault:()=>{t=!0}}),!t&&this._execute(e)}_execute(e){switch(e){case"new":return void this._editor.setHelm("");case"open":{let e=this._doc.defaultView;if(null!=e&&"function"==typeof e.prompt){let t=e.prompt("Enter HELM string");null!==t&&this._editor.setHelm(t)}return}case"save":{let e=this._editor.getHelm();return void this._editor.fire("clipboard:copy",{format:"helm",payload:e})}case"undo":return void this._editor.undo();case"redo":return void this._editor.redo();case"eraser":return this._editor.getSelection().isEmpty?void this._editor.setMode("eraser"):void this._editor.deleteSelection();case"select":case"hbond":case"move":return void this._editor.setMode(e);case"zoom-in":return void this._editor.zoom(1.1,this._molCenterOrUndefined());case"zoom-out":return void this._editor.zoom(1/1.1,this._molCenterOrUndefined());case"fit":return void this._editor.fitToContent();case"clean":return void this._editor.cleanLayout();case"find":return void this._editor.openFindReplace();case"theme":{let e=this._editor,t="function"==typeof e._currentTheme?e._currentTheme():null,i=null!==t&&"dark"===t.name;return void this._editor.setTheme(i?Dt:Ft)}default:return}}_refreshHistoryState(){this.setButtonEnabled("undo",this._editor.canUndo()),this.setButtonEnabled("redo",this._editor.canRedo())}_molCenterOrUndefined(){let e=this._editor.getMol();if(0===e.atoms.length)return;let t=e.atoms[0].p.x,i=t,n=e.atoms[0].p.y,o=n;for(let r=1;r<e.atoms.length;r++){let s=e.atoms[r].p;s.x<t&&(t=s.x),s.x>i&&(i=s.x),s.y<n&&(n=s.y),s.y>o&&(o=s.y)}return{x:(t+i)/2,y:(n+o)/2}}_reflectMode(){let e=this._editor.getMode();for(let t of["select","eraser","hbond","move"]){let i=this._buttons.get(t);if(void 0===i)continue;let n=(i.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-toolbar__btn--active"!==e).join(" ");i.setAttribute("class",t===e?`${n} hw-toolbar__btn--active`:n)}}},oo=class{constructor(e,t,i){this._unsubs=[],this._destroyed=!1,this._editor=t,this._doc=i?.documentImpl??Xi(e),this._content=Qi(this._doc,"pre",{class:"hw-pane__content hw-pane__sequence","data-testid":"sequence-pane-content"}),this.element=Qi(this._doc,"div",{class:"hw-pane hw-pane--sequence","data-testid":"pane-sequence"},[this._content]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on("helm:changed",()=>this.refresh())),this._unsubs.push(t.on("mol:changed",()=>this.refresh()))}refresh(){if(this._destroyed)return;let e=this._compute();for(;null!==this._content.firstChild;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e))}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_compute(){let e,t=this._editor.getMol(),i=[];for(let n of t.atoms){let t=n.bio.chainId;void 0!==e&&t!==e&&i.push("|"),e=t;let o=n.monomer?.naturalAnalog;i.push(void 0!==o&&""!==o?o:n.symbol)}return i.join("")}},ro=class{constructor(e,t,i){this._unsubs=[],this._destroyed=!1,this._suppressNext=!1,this._editor=t,this._doc=i?.documentImpl??Xi(e),this._input=Qi(this._doc,"div",{class:"hw-pane__content hw-pane__notation",contenteditable:"true",spellcheck:"false","data-testid":"notation-pane-content"}),this._error=Qi(this._doc,"div",{class:"hw-pane__error","data-testid":"notation-pane-error"}),this.element=Qi(this._doc,"div",{class:"hw-pane hw-pane--notation","data-testid":"pane-helm"},[this._input,this._error]),e.appendChild(this.element),this.refresh(),this._input.addEventListener("blur",()=>this._commit()),this._input.addEventListener("keydown",e=>{"Enter"===e.key&&(e.preventDefault(),e.stopPropagation(),e.stopImmediatePropagation(),this._commit())}),this._unsubs.push(t.on("helm:changed",()=>{this._suppressNext?this._suppressNext=!1:this.refresh()})),this._unsubs.push(t.on("mol:changed",()=>this.refresh()))}refresh(){if(this._destroyed)return;let e=this._editor.getHelm();for(;null!==this._input.firstChild;)this._input.removeChild(this._input.firstChild);this._input.appendChild(this._doc.createTextNode(e)),this._clearError()}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_commit(){if(this._destroyed)return;let e=(this._input.textContent??"").trim();if(e===this._editor.getHelm())return void this._clearError();let t=this._editor.getService().validate(e).filter(e=>"error"===e.severity);t.length>0?this._showError(t.map(e=>e.message).join("; ")):(this._clearError(),this._suppressNext=!0,this._editor.setHelm(e))}_showError(e){for(;null!==this._error.firstChild;)this._error.removeChild(this._error.firstChild);this._error.appendChild(this._doc.createTextNode(e)),this._error.setAttribute("class","hw-pane__error hw-pane__error--visible")}_clearError(){for(;null!==this._error.firstChild;)this._error.removeChild(this._error.firstChild);this._error.setAttribute("class","hw-pane__error")}},so=class{constructor(e,t,i){this._unsubs=[],this._destroyed=!1,this._editor=t,this._doc=i?.documentImpl??Xi(e),this._body=Qi(this._doc,"div",{class:"hw-pane__content hw-pane__properties","data-testid":"properties-pane-content"}),this.element=Qi(this._doc,"div",{class:"hw-pane hw-pane--properties","data-testid":"pane-properties"},[this._body]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on("helm:changed",()=>this.refresh())),this._unsubs.push(t.on("mol:changed",()=>this.refresh()))}refresh(){if(this._destroyed)return;for(;null!==this._body.firstChild;)this._body.removeChild(this._body.firstChild);let e=this._editor.getHelm();if(e.length>1e3)return void this._body.appendChild(Qi(this._doc,"div",{class:"hw-pane__placeholder"},["(too long)"]));let t=this._editor.getService(),i="",n=0,o=0;try{let o=t.getFormula(e);i=function(e){let t=Array.from(e.keys()).sort((e,t)=>e===t?0:"C"===e?-1:"C"===t?1:"H"===e?-1:"H"===t?1:e.localeCompare(t)),i="";for(let n of t){let t=e.get(n);void 0===t||0===t||(i+=1===t?n:`${n}${t}`)}return""===i?"—":i}(o.elements),n=o.mw}catch{i="—"}try{n=t.getMolWeight(e)}catch{}try{o=t.getExtinctionCoefficient(e)}catch{}this._body.appendChild(this._makeRow("Formula",i,"formula")),this._body.appendChild(this._makeRow("Molecular Weight",0===n?"—":n.toFixed(2),"mw")),this._body.appendChild(this._makeRow("Extinction Coefficient",0===o?"—":o.toFixed(0),"extinction"))}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_makeRow(e,t,i){let n=Qi(this._doc,"span",{class:"hw-pane__prop-label"},[e]),o=Qi(this._doc,"span",{class:"hw-pane__prop-value","data-testid":`properties-${i}`},[t]);return Qi(this._doc,"div",{class:"hw-pane__prop-row"},[n,o])}},ao=class{constructor(e,t,i){this._unsubs=[],this._destroyed=!1,this._refreshToken=0,this._editor=t,this._doc=i?.documentImpl??Xi(e),this._content=Qi(this._doc,"pre",{class:"hw-pane__content hw-pane__atomic","data-testid":"atomic-pane-content"}),this.element=Qi(this._doc,"div",{class:"hw-pane hw-pane--atomic","data-testid":"pane-atomic"},[this._content]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on("helm:changed",()=>{this.refresh()}))}async refresh(){if(this._destroyed)return;let e=++this._refreshToken,t=this._editor.getHelm(),i=this._editor.getService();if(i.hasAtomicMolfileProvider())try{let n=await i.getAtomicMolfile(t);if(this._destroyed||e!==this._refreshToken)return;this._render(n)}catch(t){if(this._destroyed||e!==this._refreshToken)return;let i=t instanceof Error?t.message:String(t);this._render(`Atomic structure unavailable: ${i}`)}else this._render("Atomic structure unavailable")}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_render(e){for(;null!==this._content.firstChild;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e))}};function lo(e){return e.toLowerCase().replace(/[^a-z0-9]+/g,"-").replace(/^-|-$/g,"")}var ho=class{constructor(e,t,i,n,o){this._unsubs=[],this._destroyed=!1,this._active=!1,this._dirty=!0,this._refreshToken=0,this._editor=t,this._provider=n,this.name=i,this._doc=o?.documentImpl??Xi(e);let r=lo(i);this._content=Qi(this._doc,"div",{class:"hw-pane__content hw-pane__extra","data-testid":`extra-pane-content-${r}`}),this.element=Qi(this._doc,"div",{class:"hw-pane hw-pane--extra","data-testid":`pane-extra-${r}`},[this._content]),e.appendChild(this.element),this._unsubs.push(t.on("helm:changed",()=>{this._dirty=!0,this._active&&this.refresh()}))}setActive(e){this._active=e,e&&this._dirty&&this.refresh()}async refresh(){if(this._destroyed)return;let e=++this._refreshToken;this._dirty=!1;let t=this._editor.getHelm();try{let i=await this._provider(t);if(this._destroyed||e!==this._refreshToken)return;this._mount(i)}catch(t){if(this._destroyed||e!==this._refreshToken)return;let i=t instanceof Error?t.message:String(t);this._renderText(`Pane "${this.name}" failed: ${i}`)}}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element)}}_mount(e){for(;null!==this._content.firstChild;)this._content.removeChild(this._content.firstChild);this._content.appendChild(e)}_renderText(e){for(;null!==this._content.firstChild;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e))}};function co(e){return"extra:"+e}var uo=[{id:"sequence",label:"Sequence"},{id:"helm",label:"HELM"},{id:"properties",label:"Properties"},{id:"atomic",label:"Atomic Structure"}],po=class{constructor(e,t){this._paneByName=new Map,this._tabsByName=new Map,this._unsubs=[],this._activePane="helm",this._destroyed=!1,this._statusModeNode=null,this._statusMessageNode=null,this._statusMessageTimeout=null,this._host=e,this._doc=t.documentImpl??Xi(e);let i="dark"===(t.theme??Dt).name?"hw-app hw-app--dark":"hw-app";this.element=Qi(this._doc,"div",{class:i,"data-testid":"app-root"}),this._toolbarHost=Qi(this._doc,"div",{class:"hw-app__toolbar"}),this._paletteHost=Qi(this._doc,"div",{class:"hw-app__palette"}),this._canvasHost=Qi(this._doc,"div",{class:"hw-app__canvas","data-testid":"canvas-host"});let n=Qi(this._doc,"div",{class:"hw-app__main"},[this._paletteHost,this._canvasHost]);this._tabsHost=Qi(this._doc,"div",{class:"hw-app__tabs",role:"tablist"}),this._paneBody=Qi(this._doc,"div",{class:"hw-app__pane-body"});let o=Qi(this._doc,"div",{class:"hw-app__panes"},[this._tabsHost,this._paneBody]);this.element.appendChild(this._toolbarHost),this.element.appendChild(n),this.element.appendChild(o),e.appendChild(this.element);let r={service:t.service};void 0!==t.initialHelm&&(r.initialHelm=t.initialHelm),void 0!==t.width&&(r.width=t.width),void 0!==t.height&&(r.height=t.height),this.canvas=new Ln(this._canvasHost,r),void 0!==t.theme&&this.canvas.setTheme(t.theme);let s={documentImpl:this._doc};void 0!==t.toolbarButtons&&(s.buttons=t.toolbarButtons),this.toolbar=new no(this._toolbarHost,this.canvas,s),this.palette=new Zn(this._paletteHost,this.canvas,{documentImpl:this._doc,...t.paletteOptions}),this.sequencePane=new oo(this._paneBody,this.canvas,{documentImpl:this._doc}),this.notationPane=new ro(this._paneBody,this.canvas,{documentImpl:this._doc}),this.propertiesPane=new so(this._paneBody,this.canvas,{documentImpl:this._doc}),t.service.hasAtomicMolfileProvider()?this.atomicStructurePane=new ao(this._paneBody,this.canvas,{documentImpl:this._doc}):this.atomicStructurePane=null,this._paneByName.set("sequence",this.sequencePane.element),this._paneByName.set("helm",this.notationPane.element),this._paneByName.set("properties",this.propertiesPane.element),null!==this.atomicStructurePane&&this._paneByName.set("atomic",this.atomicStructurePane.element);let a=[];for(let[e,i]of t.service.getExtraPanes()){let t=new ho(this._paneBody,this.canvas,e,i,{documentImpl:this._doc});a.push(t),this._paneByName.set(co(e),t.element)}this.extraPanes=a;let l=this._resolveVisiblePanes(t),h=[];for(let e of l){let t=uo.find(t=>t.id===e);void 0!==t&&h.push({id:t.id,label:t.label,testid:`tab-${t.id}`})}for(let e of a)h.push({id:co(e.name),label:e.name,testid:`tab-extra-${lo(e.name)}`});for(let{id:e,label:t,testid:i}of h){let n=this._doc.createElement("button");n.setAttribute("type","button"),n.setAttribute("class","hw-app__tab"),n.setAttribute("role","tab"),n.setAttribute("data-pane",e),n.setAttribute("data-testid",i),n.appendChild(this._doc.createTextNode(t)),n.addEventListener("click",()=>this.activatePane(e)),this._tabsHost.appendChild(n),this._tabsByName.set(e,n)}let d=l.includes("helm")?"helm":l[0]??"helm";this.activatePane(d),this._unsubs.push(this.canvas.on("theme:change",e=>this._applyTheme(e.theme))),this._buildStatusBar(),this._applyMode(this.canvas.getMode()),this._unsubs.push(this.canvas.on("option:change",e=>{"mode"===e.key&&this._applyMode(e.newValue),"nextAdd"===e.key&&this._refreshStatus()})),this._unsubs.push(this.canvas.on("mol:changed",()=>this._refreshStatus())),this._unsubs.push(this.canvas.on("helm:changed",()=>this._refreshStatus())),this._unsubs.push(this.canvas.on("editor:status",e=>{this._showStatusMessage(e.message,e.severity,e.durationMs)})),this._unsubs.push(this.canvas.on("monomer:contextmenu",e=>{e.preventDefault(),this.canvas.openAtomProps(e.atom)})),this._unsubs.push(this.canvas.on("bond:contextmenu",e=>{e.preventDefault(),this.canvas.openBondProps(e.bond)})),this._onDocKeydown=e=>this._handleEscape(e),this._doc.addEventListener("keydown",this._onDocKeydown,!0)}_handleEscape(e){let t=e;"Escape"===t.key&&(on(this._doc),hn.closeTopmost()&&(t.stopImmediatePropagation?.(),t.preventDefault?.()))}_buildStatusBar(){let e=Qi(this._doc,"div",{class:"hw-status-bar","data-testid":"status-bar"}),t=Qi(this._doc,"span",{class:"hw-status-bar__mode","data-testid":"status-mode"}),i=Qi(this._doc,"span",{class:"hw-status-bar__message","data-testid":"status-message",role:"status","aria-live":"polite"});e.appendChild(t),e.appendChild(i),this._canvasHost.appendChild(e),this._statusModeNode=t,this._statusMessageNode=i,this._refreshStatus()}_refreshStatus(){let e=this._statusModeNode;if(null===e)return;let t=this.canvas.getMode(),i=this.canvas.getNextAddSymbol();for(;null!==e.firstChild;)e.removeChild(e.firstChild);if(null===i)return void e.appendChild(this._doc.createTextNode(`Mode: ${t} | Next add: none`));e.appendChild(this._doc.createTextNode(`Mode: ${t} | Next add: `));let n=Qi(this._doc,"span",{class:"hw-status-bar__next-add-symbol","data-testid":"status-next-add-symbol"},[i.symbol]);e.appendChild(n);let o=Qi(this._doc,"button",{type:"button",class:"hw-status-bar__next-add-clear","data-testid":"status-next-add-clear","aria-label":"Clear next-add monomer",title:"Clear (Esc)"},["×"]);o.addEventListener("click",e=>{e.preventDefault(),e.stopPropagation(),this.canvas.setNextAddSymbol(null)}),e.appendChild(o)}_showStatusMessage(e,t,i){let n=this._statusMessageNode;if(null!==n){for(null!==this._statusMessageTimeout&&(clearTimeout(this._statusMessageTimeout),this._statusMessageTimeout=null);null!==n.firstChild;)n.removeChild(n.firstChild);n.appendChild(this._doc.createTextNode(e)),n.setAttribute("data-severity",t),i>0&&(this._statusMessageTimeout=setTimeout(()=>{let e=this._statusMessageNode;if(null!==e){for(;null!==e.firstChild;)e.removeChild(e.firstChild);e.removeAttribute("data-severity"),this._statusMessageTimeout=null}},i))}}_applyMode(e){let t=this._canvasHost.querySelector(".hw-editor-view");if(null===t)return;let i=(t.getAttribute("class")??"").split(/\s+/).filter(e=>!e.startsWith("hw-editor-view--")).join(" ");t.setAttribute("class",`${i} hw-editor-view--${e}`.trim()),this._refreshStatus()}setHelm(e){this.canvas.setHelm(e)}getHelm(){return this.canvas.getHelm()}on(e,t){return this.canvas.on(e,t)}activatePane(e){if(this._paneByName.has(e)||this._tabsByName.has(e)){this._activePane=e;for(let[t,i]of this._paneByName.entries())i.style.display=t===e?"":"none";for(let[t,i]of this._tabsByName.entries()){let n=(i.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-app__tab--active"!==e).join(" ");i.setAttribute("class",t===e?`${n} hw-app__tab--active`:n)}for(let e of this.extraPanes)e.setActive(this._activePane===co(e.name))}}getActivePane(){return this._activePane}destroy(){if(!this._destroyed){this._destroyed=!0,null!==this._statusMessageTimeout&&(clearTimeout(this._statusMessageTimeout),this._statusMessageTimeout=null),this._doc.removeEventListener("keydown",this._onDocKeydown,!0);for(let e of this._unsubs)e();for(let e of this.extraPanes)e.destroy();null!==this.atomicStructurePane&&this.atomicStructurePane.destroy(),this.propertiesPane.destroy(),this.notationPane.destroy(),this.sequencePane.destroy(),this.palette.destroy(),this.toolbar.destroy(),this.canvas.destroy(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element),this._host}}_resolveVisiblePanes(e){let t=e.service.hasAtomicMolfileProvider(),i=e.visiblePanes??["sequence","helm","properties","atomic"];return t||(i=i.filter(e=>"atomic"!==e)),i}_applyTheme(e){let t="dark"===e.name,i=(this.element.getAttribute("class")??"").split(/\s+/).filter(e=>"hw-app--dark"!==e).join(" ");this.element.setAttribute("class",t?`${i} hw-app--dark`:i)}},mo=class{constructor(e){this.T="ATOM",this.selected=e.selected,this.highlighted=e.highlighted,this.p={x:e.p.x,y:e.p.y},this.elem=e.symbol,this.bio={type:e.biotype,continuousId:e.bio.continuousId,chainId:e.bio.chainId,positionInChain:e.bio.positionInChain,...void 0!==e.bio.annotation?{annotation:e.bio.annotation}:{},...void 0!==e.bio.blobtype?{blobtype:e.bio.blobtype}:{},...void 0!==e.bio.ambiguity?{ambiguity:e.bio.ambiguity}:{},id:e.id},void 0!==e.inlineSource&&(this.inlineSource=e.inlineSource)}biotype(){return this.bio.type}},fo=class{constructor(e,t,i){this.a1=t,this.a2=i,this.r1=bo(e.r1),this.r2=bo(e.r2),this.kind=e.kind}};function bo(e){switch(e.kind){case"numeric":case"positional":return e.r;default:return 0}}function go(e){let t=[],i=new Map;for(let n of e.atoms){let e=new mo(n);t.push(e),i.set(n.id,e)}let n=[];for(let t of e.bonds){let e=i.get(t.a1.id),o=i.get(t.a2.id);void 0===e||void 0===o||n.push(new fo(t,e,o))}return{atoms:t,bonds:n,clone:t=>go(e),_internalMol:e}}var Ao=class{constructor(e,t,i){this._laidMol=null,this._currentHelm="",this._drawOptions={fontsize:14},this._noDraw=!1,this._svgEl=null,this.host=e,this._service=t,this._doc=i?.documentImpl??Xi(e),this._width=i?.width??400,this._height=i?.height??100,this._mol=b(),this._molView=go(this._mol),this.editor=this._buildEditor()}resizeEditor(e,t){this._width=e,this._height=t,this._redraw()}_buildEditor(){let e=this,t={get noDraw(){return e._noDraw},set noDraw(t){e._noDraw=t},get jsd(){return e.editor}};return{get div(){return e.host},get m(){return e._molView},set m(t){e._molView=t},get helm(){return t},get options(){return{width:e._width,height:e._height}},setData(t,i){if("helm"!==i)throw new Error(`LegacyEditorWrapper: only 'helm' format supported (got '${i}').`);e._setHelm(t)},setHelm(t){e._setHelm(t)},setMol(t){e._mol=t._internalMol,e._molView=e._buildView(e._mol),e._currentHelm=e._service.serialize(e._mol),e._redraw()},getHelm:t=>e._currentHelm,getMolfile:()=>Mi(e._mol),resize(t,i){e._width=t,e._height=i,e._redraw()},setSize(t,i){e._width=t,e._height=i,e._redraw()},redraw(){e._redraw()},reset(){e._mol=b(),e._laidMol=null,e._molView=go(e._mol),e._currentHelm="",e._removeSvg()},getFormula:t=>function(e){let t=e=>{let t=_o.indexOf(e);return-1===t?_o.length:t},i=[...e.elements.keys()].sort((e,i)=>{let n=t(e),o=t(i);return n!==o?n-o:e<i?-1:e>i?1:0}),n=[];for(let t of i){let i=e.elements.get(t);n.push(1===i?t:`${t}${i}`)}return n.join("")}(fi(e._mol)),getMolWeight:()=>wi(e._mol),getExtinctionCoefficient:()=>ki(e._mol),getDrawOptions:()=>e._drawOptions}}_setHelm(e){this._currentHelm=e;let t=this._service.parse(e,{mode:"lenient",resolveMonomers:!0});this._mol=t.mol,this._molView=this._buildView(this._mol),this._redraw()}_buildView(e){return this._laidMol=this._noDraw?null:Et(e),go(this._laidMol??e)}_redraw(){if(this._noDraw)return void this._removeSvg();if(""===this._currentHelm||null===this._laidMol)return void this._removeSvg();let e=new Set,t=new Set;for(let i of this._molView.atoms){let n=i.bio.id;void 0!==n&&(i.selected&&e.add(n),i.highlighted&&t.add(n))}let i=this._service.renderMolResult(this._laidMol,{width:this._width,height:this._height,maxScale:1/0,showIds:!0,selectedAtomIds:e,highlightedAtomIds:t});this._bakeViewToSurface(i.bbox,i.drawBox),this._mountSvg(i.svg)}_bakeViewToSurface(e,t){if(null===this._laidMol)return;let i=t.scale,n=t.x-e.x*i,o=t.y-e.y*i,r=this._laidMol.atoms,s=this._molView.atoms,a=Math.min(r.length,s.length);for(let e=0;e<a;e++){let t=r[e].p,a=s[e].p;a.x=t.x*i+n,a.y=t.y*i+o}}_mountSvg(e){this._removeSvg();let t=function(e,t,i,n){let o=function(e,t){let i=globalThis.DOMParser;if(void 0===i)return null;try{let n=(new i).parseFromString(t,"image/svg+xml").documentElement;return null==n?null:e.importNode(n,!0)}catch{return null}}(e,t);if(null!==o)return o;let r=e.createElementNS("http://www.w3.org/2000/svg","svg");return r.setAttribute("width",String(i)),r.setAttribute("height",String(n)),r}(this._doc,e,this._width,this._height);t.setAttribute("pointer-events","none"),null!==this.host.firstChild?this.host.insertBefore(t,this.host.firstChild):this.host.appendChild(t),this._svgEl=t}_removeSvg(){null!==this._svgEl&&null!==this._svgEl.parentNode&&this._svgEl.parentNode.removeChild(this._svgEl),this._svgEl=null}},_o=["C","H","N","O","S","P"],yo=class{constructor(e){this._width=0,this._height=0,this._doc=e}resize(e,t){this._width=e,this._height=t}select(){}dblclick(){}createMonomerDiv(e,t,i){let n=Qi(this._doc,"div",{"data-monomer":t,"data-biotype":i,"data-testid":`legacy-mex-monomer-${t}`});return e.appendChild(n),n}getSize(){return{width:this._width,height:this._height}}},vo=class{constructor(e,t,i){this.toolbarheight=32,this._drawOptions={fontsize:14},this._unsubs=[],this._destroyed=!1,this._host=e,this._service=t,this._doc=i?.documentImpl??Xi(e),this._width=i?.width??800,this._height=i?.height??400;let n={service:t};void 0!==i?.initialHelm&&(n.initialHelm=i.initialHelm),void 0!==i?.documentImpl&&(n.documentImpl=i.documentImpl),void 0!==i?.width&&(n.width=i.width),void 0!==i?.height&&(n.height=i.height),this._app=new po(e,n),this.sequence=this._app.sequencePane.element,this.notation=this._app.notationPane.element,this.properties={parent:this._app.propertiesPane.element},this._structureviewHost=Qi(this._doc,"div",{class:"hwe-legacy-app__structureview","data-testid":"legacy-app-structureview"}),this._structureviewWrapper=new Ao(this._structureviewHost,t,{documentImpl:this._doc}),this.structureview=this._structureviewWrapper,this.mex=new yo(this._doc),this._editorFacade=this._buildEditorFacade();let o=this._editorFacade;this.canvas={get host(){return o.div},get editor(){return o},get helm(){return o.helm},resizeEditor:(e,t)=>{this._resize(e,t)},getHelm:e=>o.getHelm(e),setHelm:e=>{o.setHelm(e)}};let r=()=>{this._structureviewWrapper.editor.setHelm(this._app.getHelm())};this._unsubs.push(this._app.canvas.on("helm:changed",r)),void 0!==i?.initialHelm&&i.initialHelm.length>0&&r()}get editorApp(){return this._app}_buildEditorFacade(){let e=this,t=this._app,i={noDraw:!1,get jsd(){return e._editorFacade}};return{get div(){return t.element},get m(){return e._currentMolView()},set m(e){null!=e&&void 0!==e._internalMol&&t.canvas.setMol(e._internalMol)},get helm(){return i},get options(){return{width:e._width,height:e._height}},setData(e,i){if("helm"!==i)throw new Error(`LegacyAppWrapper: only 'helm' format supported (got '${i}').`);t.setHelm(e)},setHelm(e){t.setHelm(e)},setMol(e){t.canvas.setMol(e._internalMol)},getHelm:e=>t.getHelm(),getMolfile:()=>e._service.getMolfile(t.getHelm()),resize(t,i){e._resize(t,i)},setSize(t,i){e._resize(t,i)},redraw(){t.canvas.redraw()},reset(){t.setHelm("")},getFormula:e=>function(e){let t=[];for(let[i,n]of e.elements.entries())t.push(1===n?i:`${i}${n}`);return t.join("")}(fi(t.canvas.getMol())),getMolWeight:()=>wi(t.canvas.getMol()),getExtinctionCoefficient:()=>ki(t.canvas.getMol()),getDrawOptions:()=>e._drawOptions}}_currentMolView(){let e=go(this._app.canvas.getMol()),t=this._app.canvas.getSelection();if(!t.isEmpty)for(let i of e.atoms){let e=i.bio.id;"number"==typeof e&&(i.selected=t.atoms.has(e))}return e}_resize(e,t){this._width=e,this._height=t,this._app.canvas.resize(e,t)}calculateSizes(){let e=wo(this._host.clientWidth,this._width),t=wo(this._host.clientHeight,this._height);this._resize(e,Math.max(50,t-this.toolbarheight))}destroy(){if(!this._destroyed){this._destroyed=!0;for(let e of this._unsubs)e();this._unsubs.length=0,this._app.destroy()}}};function wo(e,t){return"number"!=typeof e||isNaN(e)||e<=0?t:e}var xo=class{constructor(e,t,i){this._tooltip=null,this._destroyed=!1,this.name=e,this._service=t;let n=i?.documentImpl??globalThis.document??null;if(null===n)throw new Error("LegacyInputWrapper: no Document available.");this._doc=n,this._host=Qi(this._doc,"div",{class:"hwe-legacy-input","data-testid":"legacy-input-host"}),this.viewer=new Ao(this._host,t,{width:i?.editorOptions?.width??240,height:i?.editorOptions?.height??80,documentImpl:this._doc})}get value(){return this.viewer.editor.getHelm()}set value(e){this._ensureLive(),this.viewer.editor.setHelm(e)}get molValue(){return this.viewer.editor.m}set molValue(e){this._ensureLive(),this.viewer.editor.setMol(e)}redraw(){this._ensureLive(),this.viewer.editor.redraw()}showTooltip(e,t){this._ensureLive(),null!==this._tooltip&&null!==this._tooltip.parentNode&&this._tooltip.parentNode.removeChild(this._tooltip);let i=Qi(this._doc,"div",{class:"hwe-legacy-input__tooltip","data-testid":"legacy-input-tooltip",style:`position: absolute; left: ${t.p.x}px; top: ${t.p.y}px;`});"string"==typeof e?i.appendChild(this._doc.createTextNode(e)):i.appendChild(e),this._host.appendChild(i),this._tooltip=i}destroy(){this._destroyed||(this._destroyed=!0,null!==this._tooltip&&null!==this._tooltip.parentNode&&this._tooltip.parentNode.removeChild(this._tooltip),null!==this._host.parentNode&&this._host.parentNode.removeChild(this._host))}getHost(){return this._host}getTooltip(){return this._tooltip}_ensureLive(){if(this._destroyed)throw new Error("LegacyInputWrapper: this instance has been destroyed.");this._service}},Co=/^R([1-9][0-9]*)$/,ko=new Set([B.PEPTIDE,B.RNA,B.CHEM,B.BLOB]),Eo=new Set(["Backbone","Branch","Terminal","Undefined"]);function Bo(e){if("string"!=typeof e.symbol||0===e.symbol.length||"string"!=typeof e.molfile||!ko.has(e.polymerType)||!Eo.has(e.monomerType))return null;let t=[];for(let i of e.rgroups??[]){if("string"!=typeof i.label||!Co.test(i.label))continue;let e={label:i.label,capGroupName:"string"==typeof i.capGroupName?i.capGroupName:"",capGroupSMILES:ie(i)??""};"string"==typeof i.alternateId&&(e.alternateId=i.alternateId),t.push(e)}let i={symbol:e.symbol,molfile:e.molfile,polymerType:e.polymerType,monomerType:e.monomerType,rgroups:t};return"string"==typeof e.name&&(i.name=e.name),"string"==typeof e.smiles&&(i.smiles=e.smiles),"string"==typeof e.naturalAnalog&&(i.naturalAnalog=e.naturalAnalog),void 0!==e.meta&&null!==e.meta&&(i.meta={...e.meta}),"string"==typeof e.author&&(i.author=e.author),void 0!==e.createDate&&(i.createDate=e.createDate),"number"==typeof e.id&&(i.id=e.id),i}function So(e,t,i){if(e===B.PEPTIDE)return y;if(e===B.CHEM)return C;if(e===B.BLOB)return k;if(e===B.RNA){if("Branch"===t)return w;if("Backbone"===t)return"P"===i||"p"===i?x:v}return y}var Mo=class{constructor(e,t){this._cache=new Map,this._polymerTypesCache=null,this._version=0,this._base=e,this.source=t??("string"==typeof e.source?e.source:"datagrok-bridge"),this.onChanged=new I,this._unsub=function(e,t){let i=e.subscribe(t);return()=>{null!=i&&"function"==typeof i.unsubscribe&&i.unsubscribe()}}(e.onChanged,()=>{this._cache.clear(),this._polymerTypesCache=null,this._version+=1,this.onChanged.next({type:"reload"})})}get version(){return this._version}get isEmpty(){return"boolean"==typeof this._base.isEmpty?this._base.isEmpty:0===this.getPolymerTypes().length}getMonomer(e,t){let i=`${e}|${t}`;if(this._cache.has(i))return this._cache.get(i)??null;let n=this._base.getMonomer(e,t),o=null==n?null:this._enrichColors(Bo(n));return this._cache.set(i,o),o}_enrichColors(e){if(null===e)return null;let t=this._base;if("function"!=typeof t.getMonomerColors)return e;let i=So(e.polymerType,e.monomerType,e.naturalAnalog),n=null;try{n=t.getMonomerColors(i,e.symbol)}catch{n=null}if(null==n)return e;let o=n.backgroundcolor,r=n.textcolor,s=n.linecolor;if("string"!=typeof o||"string"!=typeof r||"string"!=typeof s)return e;let a={...e.meta??{},colors:{...e.meta?.colors??{},default:{line:s,text:r,background:o}}};return{...e,meta:a}}registerInlineSmilesMonomer(e,t){let i=this._base;var n;"function"==typeof i.getWebEditorMonomer&&i.getWebEditorMonomer((n=e)===B.PEPTIDE?y:n===B.RNA?v:n===B.CHEM?C:n===B.BLOB?k:y,t);let o=i.getMonomer(e,t),r=null==o?null:this._enrichColors(Bo(o));if(null===r)throw new Error(`BridgedMonomerLib: could not register inline SMILES monomer '${t}'`);return this._cache.set(`${e}|${t}`,r),this._cache.set(`${e}|${r.symbol}`,r),r}getMonomerSet(e){let t=new Map;for(let i of this.getPolymerTypes())for(let n of this.getMonomerSymbolsByType(i)){let o=this.getMonomer(i,n);null!==o&&So(o.polymerType,o.monomerType,o.naturalAnalog)===e&&t.set(n,o)}return t}getMonomerSymbolsByType(e){return this._base.getMonomerSymbolsByType(e)}getByNaturalAnalog(e,t){let i=[];for(let n of this.getMonomerSymbolsByType(e)){let o=this.getMonomer(e,n);null!==o&&o.naturalAnalog===t&&i.push(o)}return i}getPolymerTypes(){if(null!==this._polymerTypesCache)return this._polymerTypesCache;let e=[],t="function"==typeof this._base.getPolymerTypes?this._base.getPolymerTypes():Object.values(B);for(let i of t){if(!ko.has(i))continue;let t=this._base.getMonomerSymbolsByType(i);Array.isArray(t)&&t.length>0&&e.push(i)}return this._polymerTypesCache=e,e}getColors(e,t){let i="dark"===t?ee:Z;return te(e,null===e?y:So(e.polymerType,e.monomerType,e.naturalAnalog),i)}addMonomer(e){throw new Error("BridgedMonomerLib: mutation is not supported on a Datagrok-bridged library.")}removeMonomer(e,t){return!1}merge(e){throw new Error("BridgedMonomerLib: mutation is not supported on a Datagrok-bridged library.")}toJSON(){let e=[];for(let t of this.getPolymerTypes())for(let i of this.getMonomerSymbolsByType(t)){let n=this.getMonomer(t,i);null!==n&&e.push(n)}return e}destroy(){this._unsub(),this.onChanged.complete(),this._cache.clear()}};function To(e,t){return new Mo(e,t)}var Io=class e{constructor(e){if(this._overriddenFuncs=null,this._originalFuncs=null,this._molfilesEditor=null,this._molfilesEditorHost=null,this._molfilesGcTimer=null,void 0===e.service||null===e.service)throw new TypeError("HelmHelperAdapter: options.service is required");this._service=e.service,this.seqHelper=e.seqHelper??null,this._logger=e.logger??new h,this._bridge=e.monomerLibBridge??(e=>To(e)),this._doc=e.documentImpl??$o()}get service(){return this._service}createHelmInput(e,t){let i={...t};return void 0===i.documentImpl&&null!==this._doc&&(i.documentImpl=this._doc),new xo(e,this._service,i)}createHelmWebEditor(e,t){let i=e??this._createDetachedHost();return new Ao(i,this._service,{...void 0!==t?.width?{width:t.width}:{},...void 0!==t?.height?{height:t.height}:{},...null!==this._doc?{documentImpl:this._doc}:{}})}createWebEditorApp(e,t){return new vo(e,this._service,{...void 0!==t?{initialHelm:t}:{},...null!==this._doc?{documentImpl:this._doc}:{}})}get originalMonomersFuncs(){return this._originalFuncs}buildMonomersFuncsFromLib(e){let t=this._bridge(e),i=e;return{getMonomer:function(e,n){if("function"==typeof i.getWebEditorMonomer){let t=i.getWebEditorMonomer(e,n);if(null!=t)return t}let{biotype:o,symbol:r}=Po(e,n);if(null===r)return null;let s=(h=r).length>=2&&"["===h.charAt(0)&&"]"===h.charAt(h.length-1)?h.slice(1,h.length-1):h,a=Ro(o),l=t.getMonomer(a,s);var h;return null===l?null:Ho(l,s)},getMonomerSet:function(e){let{biotype:i}=Po(e,void 0),n=Ro(i),o={};for(let e of t.getMonomerSymbolsByType(n)){let i=t.getMonomer(n,e);null!==i&&(o[e]=Ho(i,e))}return o}}}overrideMonomersFuncs(e){let t=this._overriddenFuncs;return null===this._originalFuncs&&(this._originalFuncs=t??this._defaultFuncs()),this._overriddenFuncs=e,t??this._originalFuncs}revertOriginalMonomersFuncs(){let e=this._originalFuncs??this._defaultFuncs(),t=this._overriddenFuncs??e;return this._overriddenFuncs=e,this._originalFuncs=null,t}getHoveredAtom(e,t,i,n){let o=new Yi(i._internalMol,Dt).test({x:e,y:t});if(null===o||void 0===o.atom)return null;for(let e of i.atoms)if(e.bio.id===o.atom.id||void 0===e.bio.id&&e.bio.continuousId===o.atom.bio.continuousId)return e;return null}getMolfiles(e){let t=this._ensureMolfilesEditor();t.editor.helm.noDraw=!0;try{let i=[];for(let n of e)"string"==typeof n&&0!==n.length?(t.editor.setHelm(n),i.push(t.editor.getMolfile())):i.push("");return i}finally{t.editor.helm.noDraw=!1,this._scheduleMolfilesEditorGc()}}parse(e,t){return go(Et(this._service.parse(e,{mode:"lenient",resolveMonomers:!1}).mol))}removeGaps(e){let t;try{t=this._service.removeGaps(e)}catch(e){throw e instanceof a&&void 0===e.type&&(e.type="HelmNotSupportedError"),e}let i=function(e,t){try{let i=e.parse(t,{mode:"lenient",resolveMonomers:!1});for(let e of i.mol.atoms)if("*"===e.symbol)return!0;return!1}catch{return!1}}(this._service,e);return{srcHelm:t.srcHelm,resHelm:t.resHelm,monomerMap:i?new Map(t.monomerMap):null}}destroy(){null!==this._molfilesGcTimer&&(clearTimeout(this._molfilesGcTimer),this._molfilesGcTimer=null),this._removeMolfilesEditorNow()}_defaultFuncs(){return{getMonomer:(e,t)=>null,getMonomerSet:e=>({})}}_createDetachedHost(){let e=this._doc??$o();if(null===e)throw new Error("HelmHelperAdapter: no Document available");let t=e.createElement("div");return t.style.width="0px",t.style.height="0px",t.style.position="fixed",t}_ensureMolfilesEditor(){if(null!==this._molfilesEditor)return null!==this._molfilesGcTimer&&(clearTimeout(this._molfilesGcTimer),this._molfilesGcTimer=null),this._molfilesEditor;let e=this._createDetachedHost();return this._molfilesEditorHost=e,this._molfilesEditor=new 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b&&(b.fetch="get"),this.get(e,{allowStale:i,updateAgeOnGet:n,noDeleteOnStaleGet:o,status:b});const A={allowStale:i,updateAgeOnGet:n,noDeleteOnStaleGet:o,ttl:r,noDisposeOnSet:s,size:a,sizeCalculation:l,noUpdateTTL:h,noDeleteOnFetchRejection:d,allowStaleOnFetchRejection:c,allowStaleOnFetchAbort:p,ignoreFetchAbort:u,status:b,signal:g};let _=this.#h.get(e);if(void 0===_){b&&(b.fetch="miss");const t=this.#k(e,_,A,m);return t.__returned=t}{const t=this.#c[_];if(this.#C(t)){const e=i&&void 0!==t.__staleWhileFetching;return b&&(b.fetch="inflight",e&&(b.returnedStale=!0)),e?t.__staleWhileFetching:t.__returned=t}const o=this.#M(_);if(!f&&!o)return b&&(b.fetch="hit"),this.#E(_),n&&this.#P(_),b&&this.#R(b,_),t;const r=this.#k(e,_,A,m),s=void 0!==r.__staleWhileFetching&&i;return b&&(b.fetch=o?"stale":"refresh",s&&o&&(b.returnedStale=!0)),s?r.__staleWhileFetching:r.__returned=r}}async forceFetch(e,t={}){const i=await this.fetch(e,t);if(void 0===i)throw new Error("fetch() returned undefined");return i}memo(e,t={}){const i=this.#s;if(!i)throw new Error("no memoMethod provided to constructor");const{context:n,forceRefresh:o,...r}=t,s=this.get(e,r);if(!o&&void 0!==s)return s;const a=i(e,s,{options:r,context:n});return this.set(e,a,r),a}get(e,t={}){const{allowStale:i=this.allowStale,updateAgeOnGet:n=this.updateAgeOnGet,noDeleteOnStaleGet:o=this.noDeleteOnStaleGet,status:r}=t,s=this.#h.get(e);if(void 0!==s){const t=this.#c[s],a=this.#C(t);return r&&this.#R(r,s),this.#M(s)?(r&&(r.get="stale"),a?(r&&i&&void 0!==t.__staleWhileFetching&&(r.returnedStale=!0),i?t.__staleWhileFetching:void 0):(o||this.#$(e,"expire"),r&&i&&(r.returnedStale=!0),i?t:void 0)):(r&&(r.get="hit"),a?t.__staleWhileFetching:(this.#E(s),n&&this.#P(s),t))}r&&(r.get="miss")}#z(e,t){this.#p[t]=e,this.#u[e]=t}#E(e){e!==this.#f&&(e===this.#m?this.#m=this.#u[e]:this.#z(this.#p[e],this.#u[e]),this.#z(this.#f,e),this.#f=e)}delete(e){return this.#$(e,"delete")}#$(e,t){let i=!1;if(0!==this.#a){const n=this.#h.get(e);if(void 0!==n)if(i=!0,1===this.#a)this.#G(t);else{this.#H(n);const i=this.#c[n];if(this.#C(i)?i.__abortController.abort(new Error("deleted")):(this.#v||this.#x)&&(this.#v&&this.#n?.(i,e,t),this.#x&&this.#g?.push([i,e,t])),this.#h.delete(e),this.#d[n]=void 0,this.#c[n]=void 0,n===this.#f)this.#f=this.#p[n];else if(n===this.#m)this.#m=this.#u[n];else{const e=this.#p[n];this.#u[e]=this.#u[n];const t=this.#u[n];this.#p[t]=this.#p[n]}this.#a--,this.#b.push(n)}}if(this.#x&&this.#g?.length){const e=this.#g;let t;for(;t=e?.shift();)this.#o?.(...t)}return i}clear(){return this.#G("delete")}#G(e){for(const t of this.#S({allowStale:!0})){const i=this.#c[t];if(this.#C(i))i.__abortController.abort(new Error("deleted"));else{const n=this.#d[t];this.#v&&this.#n?.(i,n,e),this.#x&&this.#g?.push([i,n,e])}}if(this.#h.clear(),this.#c.fill(void 0),this.#d.fill(void 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