@e-infra/react-molstar-wrapper 0.0.8 → 0.0.9

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Files changed (14) hide show
  1. package/README.md +438 -9
  2. package/dist/index.cjs.js +71 -6
  3. package/dist/index.cjs.js.map +1 -1
  4. package/dist/index.es.js +71 -6
  5. package/dist/index.es.js.map +1 -1
  6. package/dist/types/core/Plugin.d.ts +8 -1
  7. package/dist/types/core/Plugin.d.ts.map +1 -1
  8. package/dist/types/core/types.d.ts +1 -1
  9. package/dist/types/core/types.d.ts.map +1 -1
  10. package/dist/types/react/Viewer.d.ts +10 -5
  11. package/dist/types/react/Viewer.d.ts.map +1 -1
  12. package/dist/types/react/types.d.ts +1 -0
  13. package/dist/types/react/types.d.ts.map +1 -1
  14. package/package.json +15 -16
package/dist/index.cjs.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.cjs.js","sources":["../node_modules/react/cjs/react-jsx-runtime.production.js","../node_modules/react/cjs/react-jsx-runtime.development.js","../node_modules/react/jsx-runtime.js","../lib/react/LoaderView.tsx","../lib/react/ErrorView.tsx","../lib/core/Plugin.ts","../lib/core/Manager.ts","../lib/core/tree/chopping.ts","../lib/core/tree/colors.ts","../lib/core/tree/selectors.ts","../lib/core/tree/rendering.ts","../lib/core/tree/create-mvs.ts","../lib/react/Viewer.tsx"],"sourcesContent":["/**\n * @license React\n * react-jsx-runtime.production.js\n *\n * Copyright (c) Meta Platforms, Inc. and affiliates.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\n\"use strict\";\nvar REACT_ELEMENT_TYPE = Symbol.for(\"react.transitional.element\"),\n REACT_FRAGMENT_TYPE = Symbol.for(\"react.fragment\");\nfunction jsxProd(type, config, maybeKey) {\n var key = null;\n void 0 !== maybeKey && (key = \"\" + maybeKey);\n void 0 !== config.key && (key = \"\" + config.key);\n if (\"key\" in config) {\n maybeKey = {};\n for (var propName in config)\n \"key\" !== propName && (maybeKey[propName] = config[propName]);\n } else maybeKey = config;\n config = maybeKey.ref;\n return {\n $$typeof: REACT_ELEMENT_TYPE,\n type: type,\n key: key,\n ref: void 0 !== config ? config : null,\n props: maybeKey\n };\n}\nexports.Fragment = REACT_FRAGMENT_TYPE;\nexports.jsx = jsxProd;\nexports.jsxs = jsxProd;\n","/**\n * @license React\n * react-jsx-runtime.development.js\n *\n * Copyright (c) Meta Platforms, Inc. and affiliates.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\n\"use strict\";\n\"production\" !== process.env.NODE_ENV &&\n (function () {\n function getComponentNameFromType(type) {\n if (null == type) return null;\n if (\"function\" === typeof type)\n return type.$$typeof === REACT_CLIENT_REFERENCE\n ? null\n : type.displayName || type.name || null;\n if (\"string\" === typeof type) return type;\n switch (type) {\n case REACT_FRAGMENT_TYPE:\n return \"Fragment\";\n case REACT_PROFILER_TYPE:\n return \"Profiler\";\n case REACT_STRICT_MODE_TYPE:\n return \"StrictMode\";\n case REACT_SUSPENSE_TYPE:\n return \"Suspense\";\n case REACT_SUSPENSE_LIST_TYPE:\n return \"SuspenseList\";\n case REACT_ACTIVITY_TYPE:\n return \"Activity\";\n }\n if (\"object\" === typeof type)\n switch (\n (\"number\" === typeof type.tag &&\n console.error(\n \"Received an unexpected object in getComponentNameFromType(). This is likely a bug in React. Please file an issue.\"\n ),\n type.$$typeof)\n ) {\n case REACT_PORTAL_TYPE:\n return \"Portal\";\n case REACT_CONTEXT_TYPE:\n return type.displayName || \"Context\";\n case REACT_CONSUMER_TYPE:\n return (type._context.displayName || \"Context\") + \".Consumer\";\n case REACT_FORWARD_REF_TYPE:\n var innerType = type.render;\n type = type.displayName;\n type ||\n ((type = innerType.displayName || innerType.name || \"\"),\n (type = \"\" !== type ? \"ForwardRef(\" + type + \")\" : \"ForwardRef\"));\n return type;\n case REACT_MEMO_TYPE:\n return (\n (innerType = type.displayName || null),\n null !== innerType\n ? innerType\n : getComponentNameFromType(type.type) || \"Memo\"\n );\n case REACT_LAZY_TYPE:\n innerType = type._payload;\n type = type._init;\n try {\n return getComponentNameFromType(type(innerType));\n } catch (x) {}\n }\n return null;\n }\n function testStringCoercion(value) {\n return \"\" + value;\n }\n function checkKeyStringCoercion(value) {\n try {\n testStringCoercion(value);\n var JSCompiler_inline_result = !1;\n } catch (e) {\n JSCompiler_inline_result = !0;\n }\n if (JSCompiler_inline_result) {\n JSCompiler_inline_result = console;\n var JSCompiler_temp_const = JSCompiler_inline_result.error;\n var JSCompiler_inline_result$jscomp$0 =\n (\"function\" === typeof Symbol &&\n Symbol.toStringTag &&\n value[Symbol.toStringTag]) ||\n value.constructor.name ||\n \"Object\";\n JSCompiler_temp_const.call(\n JSCompiler_inline_result,\n \"The provided key is an unsupported type %s. This value must be coerced to a string before using it here.\",\n JSCompiler_inline_result$jscomp$0\n );\n return testStringCoercion(value);\n }\n }\n function getTaskName(type) {\n if (type === REACT_FRAGMENT_TYPE) return \"<>\";\n if (\n \"object\" === typeof type &&\n null !== type &&\n type.$$typeof === REACT_LAZY_TYPE\n )\n return \"<...>\";\n try {\n var name = getComponentNameFromType(type);\n return name ? \"<\" + name + \">\" : \"<...>\";\n } catch (x) {\n return \"<...>\";\n }\n }\n function getOwner() {\n var dispatcher = ReactSharedInternals.A;\n return null === dispatcher ? null : dispatcher.getOwner();\n }\n function UnknownOwner() {\n return Error(\"react-stack-top-frame\");\n }\n function hasValidKey(config) {\n if (hasOwnProperty.call(config, \"key\")) {\n var getter = Object.getOwnPropertyDescriptor(config, \"key\").get;\n if (getter && getter.isReactWarning) return !1;\n }\n return void 0 !== config.key;\n }\n function defineKeyPropWarningGetter(props, displayName) {\n function warnAboutAccessingKey() {\n specialPropKeyWarningShown ||\n ((specialPropKeyWarningShown = !0),\n console.error(\n \"%s: `key` is not a prop. Trying to access it will result in `undefined` being returned. If you need to access the same value within the child component, you should pass it as a different prop. (https://react.dev/link/special-props)\",\n displayName\n ));\n }\n warnAboutAccessingKey.isReactWarning = !0;\n Object.defineProperty(props, \"key\", {\n get: warnAboutAccessingKey,\n configurable: !0\n });\n }\n function elementRefGetterWithDeprecationWarning() {\n var componentName = getComponentNameFromType(this.type);\n didWarnAboutElementRef[componentName] ||\n ((didWarnAboutElementRef[componentName] = !0),\n console.error(\n \"Accessing element.ref was removed in React 19. ref is now a regular prop. It will be removed from the JSX Element type in a future release.\"\n ));\n componentName = this.props.ref;\n return void 0 !== componentName ? componentName : null;\n }\n function ReactElement(type, key, props, owner, debugStack, debugTask) {\n var refProp = props.ref;\n type = {\n $$typeof: REACT_ELEMENT_TYPE,\n type: type,\n key: key,\n props: props,\n _owner: owner\n };\n null !== (void 0 !== refProp ? refProp : null)\n ? Object.defineProperty(type, \"ref\", {\n enumerable: !1,\n get: elementRefGetterWithDeprecationWarning\n })\n : Object.defineProperty(type, \"ref\", { enumerable: !1, value: null });\n type._store = {};\n Object.defineProperty(type._store, \"validated\", {\n configurable: !1,\n enumerable: !1,\n writable: !0,\n value: 0\n });\n Object.defineProperty(type, \"_debugInfo\", {\n configurable: !1,\n enumerable: !1,\n writable: !0,\n value: null\n });\n Object.defineProperty(type, \"_debugStack\", {\n configurable: !1,\n enumerable: !1,\n writable: !0,\n value: debugStack\n });\n Object.defineProperty(type, \"_debugTask\", {\n configurable: !1,\n enumerable: !1,\n writable: !0,\n value: debugTask\n });\n Object.freeze && (Object.freeze(type.props), Object.freeze(type));\n return type;\n }\n function jsxDEVImpl(\n type,\n config,\n maybeKey,\n isStaticChildren,\n debugStack,\n debugTask\n ) {\n var children = config.children;\n if (void 0 !== children)\n if (isStaticChildren)\n if (isArrayImpl(children)) {\n for (\n isStaticChildren = 0;\n isStaticChildren < children.length;\n isStaticChildren++\n )\n validateChildKeys(children[isStaticChildren]);\n Object.freeze && Object.freeze(children);\n } else\n console.error(\n \"React.jsx: Static children should always be an array. You are likely explicitly calling React.jsxs or React.jsxDEV. Use the Babel transform instead.\"\n );\n else validateChildKeys(children);\n if (hasOwnProperty.call(config, \"key\")) {\n children = getComponentNameFromType(type);\n var keys = Object.keys(config).filter(function (k) {\n return \"key\" !== k;\n });\n isStaticChildren =\n 0 < keys.length\n ? \"{key: someKey, \" + keys.join(\": ..., \") + \": ...}\"\n : \"{key: someKey}\";\n didWarnAboutKeySpread[children + isStaticChildren] ||\n ((keys =\n 0 < keys.length ? \"{\" + keys.join(\": ..., \") + \": ...}\" : \"{}\"),\n console.error(\n 'A props object containing a \"key\" prop is being spread into JSX:\\n let props = %s;\\n <%s {...props} />\\nReact keys must be passed directly to JSX without using spread:\\n let props = %s;\\n <%s key={someKey} {...props} />',\n isStaticChildren,\n children,\n keys,\n children\n ),\n (didWarnAboutKeySpread[children + isStaticChildren] = !0));\n }\n children = null;\n void 0 !== maybeKey &&\n (checkKeyStringCoercion(maybeKey), (children = \"\" + maybeKey));\n hasValidKey(config) &&\n (checkKeyStringCoercion(config.key), (children = \"\" + config.key));\n if (\"key\" in config) {\n maybeKey = {};\n for (var propName in config)\n \"key\" !== propName && (maybeKey[propName] = config[propName]);\n } else maybeKey = config;\n children &&\n defineKeyPropWarningGetter(\n maybeKey,\n \"function\" === typeof type\n ? type.displayName || type.name || \"Unknown\"\n : type\n );\n return ReactElement(\n type,\n children,\n maybeKey,\n getOwner(),\n debugStack,\n debugTask\n );\n }\n function validateChildKeys(node) {\n isValidElement(node)\n ? node._store && (node._store.validated = 1)\n : \"object\" === typeof node &&\n null !== node &&\n node.$$typeof === REACT_LAZY_TYPE &&\n (\"fulfilled\" === node._payload.status\n ? isValidElement(node._payload.value) &&\n node._payload.value._store &&\n (node._payload.value._store.validated = 1)\n : node._store && (node._store.validated = 1));\n }\n function isValidElement(object) {\n return (\n \"object\" === typeof object &&\n null !== object &&\n object.$$typeof === REACT_ELEMENT_TYPE\n );\n }\n var React = require(\"react\"),\n REACT_ELEMENT_TYPE = Symbol.for(\"react.transitional.element\"),\n REACT_PORTAL_TYPE = Symbol.for(\"react.portal\"),\n REACT_FRAGMENT_TYPE = Symbol.for(\"react.fragment\"),\n REACT_STRICT_MODE_TYPE = Symbol.for(\"react.strict_mode\"),\n REACT_PROFILER_TYPE = Symbol.for(\"react.profiler\"),\n REACT_CONSUMER_TYPE = Symbol.for(\"react.consumer\"),\n REACT_CONTEXT_TYPE = Symbol.for(\"react.context\"),\n REACT_FORWARD_REF_TYPE = Symbol.for(\"react.forward_ref\"),\n REACT_SUSPENSE_TYPE = Symbol.for(\"react.suspense\"),\n REACT_SUSPENSE_LIST_TYPE = Symbol.for(\"react.suspense_list\"),\n REACT_MEMO_TYPE = Symbol.for(\"react.memo\"),\n REACT_LAZY_TYPE = Symbol.for(\"react.lazy\"),\n REACT_ACTIVITY_TYPE = Symbol.for(\"react.activity\"),\n REACT_CLIENT_REFERENCE = Symbol.for(\"react.client.reference\"),\n ReactSharedInternals =\n React.__CLIENT_INTERNALS_DO_NOT_USE_OR_WARN_USERS_THEY_CANNOT_UPGRADE,\n hasOwnProperty = Object.prototype.hasOwnProperty,\n isArrayImpl = Array.isArray,\n createTask = console.createTask\n ? console.createTask\n : function () {\n return null;\n };\n React = {\n react_stack_bottom_frame: function (callStackForError) {\n return callStackForError();\n }\n };\n var specialPropKeyWarningShown;\n var didWarnAboutElementRef = {};\n var unknownOwnerDebugStack = React.react_stack_bottom_frame.bind(\n React,\n UnknownOwner\n )();\n var unknownOwnerDebugTask = createTask(getTaskName(UnknownOwner));\n var didWarnAboutKeySpread = {};\n exports.Fragment = REACT_FRAGMENT_TYPE;\n exports.jsx = function (type, config, maybeKey) {\n var trackActualOwner =\n 1e4 > ReactSharedInternals.recentlyCreatedOwnerStacks++;\n return jsxDEVImpl(\n type,\n config,\n maybeKey,\n !1,\n trackActualOwner\n ? Error(\"react-stack-top-frame\")\n : unknownOwnerDebugStack,\n trackActualOwner ? createTask(getTaskName(type)) : unknownOwnerDebugTask\n );\n };\n exports.jsxs = function (type, config, maybeKey) {\n var trackActualOwner =\n 1e4 > ReactSharedInternals.recentlyCreatedOwnerStacks++;\n return jsxDEVImpl(\n type,\n config,\n maybeKey,\n !0,\n trackActualOwner\n ? Error(\"react-stack-top-frame\")\n : unknownOwnerDebugStack,\n trackActualOwner ? createTask(getTaskName(type)) : unknownOwnerDebugTask\n );\n };\n })();\n","'use strict';\n\nif (process.env.NODE_ENV === 'production') {\n module.exports = require('./cjs/react-jsx-runtime.production.js');\n} else {\n module.exports = require('./cjs/react-jsx-runtime.development.js');\n}\n","export default function LoaderView() {\n return (\n <div\n style={{\n position: \"absolute\",\n top: 0,\n left: 0,\n width: \"100%\",\n height: \"100%\",\n backdropFilter: \"blur(5px)\",\n backgroundColor: \"#0000000A\",\n }}\n >\n <div\n style={{\n position: \"absolute\",\n top: \"50%\",\n left: \"50%\",\n transform: \"translate(-50%, -50%)\",\n display: \"flex\",\n flexDirection: \"column\",\n alignItems: \"center\",\n gap: \"1rem\",\n }}\n >\n <div\n style={{\n width: \"48px\",\n height: \"48px\",\n border: \"6px solid #e5e7eb\",\n borderTopColor: \"#3b82f6\",\n borderRadius: \"50%\",\n animation: \"spin 0.8s linear infinite\",\n }}\n />\n <p\n style={{\n margin: 0,\n fontSize: \"0.875rem\",\n color: \"#6b7280\",\n fontFamily: \"system-ui, -apple-system, sans-serif\",\n }}\n >\n Loading...\n </p>\n <style>\n {`\n @keyframes spin {\n to {\n transform: rotate(360deg);\n }\n }\n `}\n </style>\n </div>\n </div>\n );\n}\n","export default function ErrorView() {\n return (\n <div\n style={{\n position: \"absolute\",\n top: 0,\n left: 0,\n width: \"100%\",\n height: \"100%\",\n backdropFilter: \"blur(5px)\",\n backgroundColor: \"#0000000A\",\n }}\n >\n <div\n style={{\n position: \"absolute\",\n top: \"50%\",\n left: \"50%\",\n transform: \"translate(-50%, -50%)\",\n display: \"flex\",\n flexDirection: \"column\",\n alignItems: \"center\",\n gap: \"0.75rem\",\n padding: \"1.5rem\",\n }}\n >\n <div\n style={{\n width: \"48px\",\n height: \"48px\",\n borderRadius: \"50%\",\n backgroundColor: \"#fef2f2\",\n display: \"flex\",\n alignItems: \"center\",\n justifyContent: \"center\",\n }}\n >\n <svg\n width=\"24\"\n height=\"24\"\n viewBox=\"0 0 24 24\"\n fill=\"none\"\n stroke=\"#ef4444\"\n strokeWidth=\"2\"\n strokeLinecap=\"round\"\n strokeLinejoin=\"round\"\n aria-label=\"Error icon\"\n >\n <title>Error</title>\n <circle cx=\"12\" cy=\"12\" r=\"10\" />\n <line x1=\"15\" y1=\"9\" x2=\"9\" y2=\"15\" />\n <line x1=\"9\" y1=\"9\" x2=\"15\" y2=\"15\" />\n </svg>\n </div>\n <div style={{ textAlign: \"center\" }}>\n <p\n style={{\n margin: 0,\n fontSize: \"0.875rem\",\n fontWeight: 600,\n color: \"#1f2937\",\n fontFamily: \"system-ui, -apple-system, sans-serif\",\n }}\n >\n Error loading viewer\n </p>\n <p\n style={{\n margin: \"0.25rem 0 0 0\",\n fontSize: \"0.75rem\",\n color: \"#6b7280\",\n fontFamily: \"system-ui, -apple-system, sans-serif\",\n }}\n >\n Please try refreshing the page\n </p>\n </div>\n </div>\n </div>\n );\n}\n","import { loadMVSData } from \"molstar/lib/extensions/mvs/components/formats\";\nimport type { MVSData } from \"molstar/lib/extensions/mvs/mvs-data.d.ts\";\nimport type { ColorHEX, Matrix3D, Vector3D } from \"./types\";\nimport { Color } from \"molstar/lib/mol-util/color\";\n\nimport { createPluginUI } from \"molstar/lib/mol-plugin-ui\";\nimport { renderReact18 } from \"molstar/lib/mol-plugin-ui/react18\";\nimport { PluginSpec } from \"molstar/lib/mol-plugin/spec\";\nimport { MolViewSpec } from \"molstar/lib/extensions/mvs/behavior\";\nimport { DefaultPluginUISpec } from \"molstar/lib/mol-plugin-ui/spec\";\nimport type { InitialUI } from \"./types\";\nimport type { PluginUIContext } from \"molstar/lib/mol-plugin-ui/context\";\nimport { Mat4, Vec3 } from \"molstar/lib/mol-math/linear-algebra\";\nimport { PluginStateObject } from \"molstar/lib/mol-plugin-state/objects\";\nimport { Script } from \"molstar/lib/mol-script/script\";\nimport {\n StructureElement,\n StructureSelection,\n} from \"molstar/lib/mol-model/structure\";\nimport { StateTransforms } from \"molstar/lib/mol-plugin-state/transforms\";\n\nclass Plugin {\n private plugin: PluginUIContext;\n private objectUrls: Set<string>;\n\n constructor(plugin: PluginUIContext) {\n this.plugin = plugin;\n this.objectUrls = new Set();\n }\n\n /**\n * Create a Plugin by instantiating the underlying PluginUI.\n * We use a static async factory because constructors cannot be async.\n */\n static async create(\n container: HTMLElement,\n initialUI: InitialUI\n ): Promise<Plugin> {\n const defaultSpec = DefaultPluginUISpec();\n\n if (!container.querySelector(\".msp-plugin\")) {\n container.innerHTML = \"\";\n }\n\n const plugin = await createPluginUI({\n target: container,\n render: renderReact18,\n spec: {\n actions: defaultSpec.actions ?? [],\n behaviors: [\n ...(initialUI !== \"minimal\" ? defaultSpec.behaviors : []),\n PluginSpec.Behavior(MolViewSpec),\n ],\n animations: [...(defaultSpec.animations || [])],\n layout: {\n initial: {\n showControls: initialUI === \"expanded\",\n controlsDisplay: \"reactive\",\n // isExpanded: false,\n },\n },\n components: {\n ...defaultSpec.components,\n },\n canvas3d: {\n ...defaultSpec.canvas3d,\n camera: {\n ...defaultSpec.canvas3d?.camera,\n helper: {\n axes:\n initialUI === \"minimal\"\n ? {\n name: \"off\",\n params: {},\n }\n : defaultSpec.canvas3d?.camera?.helper?.axes,\n },\n },\n },\n },\n });\n\n return new Plugin(plugin);\n }\n\n dispose() {\n this.plugin.dispose();\n this.cleanupObjectUrls();\n }\n\n cleanupObjectUrls() {\n for (const url of this.objectUrls) {\n try {\n URL.revokeObjectURL(url);\n } catch (_e) {\n // ignore\n }\n\n this.objectUrls.delete(url);\n }\n }\n\n createObjectUrlFromFile(file: File): string {\n const url = URL.createObjectURL(file);\n this.objectUrls.add(url);\n return url;\n }\n\n clear() {\n this.plugin.clear();\n }\n\n async loadMvs(mvs: MVSData) {\n return await loadMVSData(this.plugin, mvs, \"mvsj\");\n }\n\n setBackgroundColor(color: ColorHEX) {\n const hexString = color.replace(\"#\", \"0x\");\n\n this.plugin.canvas3d?.setProps({\n renderer: { backgroundColor: Color.fromHexString(hexString) },\n });\n }\n\n setAnimation(type: \"spin\" | \"rock\" | \"off\", speed?: number) {\n if (type === \"off\") {\n this.plugin.canvas3d?.setProps({\n trackball: {\n animate: {\n name: \"off\",\n params: {},\n },\n },\n });\n\n return;\n }\n\n const animationParams =\n type === \"spin\"\n ? {\n speed: speed ?? 0.05,\n }\n : {\n speed: speed ?? 0.2,\n angle: 10,\n };\n\n this.plugin.canvas3d?.setProps({\n trackball: {\n animate: {\n name: type,\n params: animationParams,\n },\n },\n });\n }\n\n async focusOnDomain(domainStart: number, domainEnd: number) {\n const state = this.plugin.state.data;\n\n // Find all structure cells in the state tree\n const structures = state.selectQ((q) =>\n q.rootsOfType(PluginStateObject.Molecule.Structure)\n );\n\n if (structures.length === 0) {\n return;\n }\n\n // Use the first structure for focusing\n const structureCell = structures[0];\n if (!structureCell?.obj) {\n return;\n }\n\n const structureData = structureCell.obj.data;\n\n // Build a selection query for the residue range\n const selection = Script.getStructureSelection(\n (Q) =>\n Q.struct.generator.atomGroups({\n \"residue-test\": Q.core.rel.inRange([\n Q.struct.atomProperty.macromolecular.auth_seq_id(),\n domainStart,\n domainEnd,\n ]),\n }),\n structureData\n );\n\n const loci = StructureSelection.toLociWithSourceUnits(selection);\n\n // Focus camera on the loci\n if (!StructureElement.Loci.isEmpty(loci)) {\n await this.plugin.managers.camera.focusLoci(loci);\n }\n }\n\n async resetView() {\n // Reset camera to show all structures\n await this.plugin.managers.camera.reset();\n }\n\n async updateStructureTransform(\n structureIndex: number,\n translation?: Vector3D,\n rotation?: Matrix3D\n ) {\n const state = this.plugin.state.data;\n\n // Find all structure cells in the state tree\n const structures = state.selectQ((q) =>\n q.rootsOfType(PluginStateObject.Molecule.Structure)\n );\n\n if (structureIndex >= structures.length) {\n return;\n }\n\n const targetStructure = structures[structureIndex];\n if (!targetStructure) {\n return;\n }\n\n // Find transform nodes in the structure's subtree\n const allCells = state.selectQ((q) => q.root.subtree());\n const transforms = allCells.filter(\n (cell) =>\n cell.transform.transformer ===\n StateTransforms.Model.TransformStructureConformation\n );\n\n // Match transform by structure index (assumes structures and transforms are in same order)\n const targetTransform = transforms[structureIndex];\n\n if (targetTransform) {\n // Create the transformation matrix\n const matrix = Mat4.identity();\n\n // Apply rotation if provided\n if (rotation) {\n // Set rotation part of the matrix (top-left 3x3)\n Mat4.setValue(matrix, 0, 0, rotation[0][0]);\n Mat4.setValue(matrix, 0, 1, rotation[0][1]);\n Mat4.setValue(matrix, 0, 2, rotation[0][2]);\n Mat4.setValue(matrix, 1, 0, rotation[1][0]);\n Mat4.setValue(matrix, 1, 1, rotation[1][1]);\n Mat4.setValue(matrix, 1, 2, rotation[1][2]);\n Mat4.setValue(matrix, 2, 0, rotation[2][0]);\n Mat4.setValue(matrix, 2, 1, rotation[2][1]);\n Mat4.setValue(matrix, 2, 2, rotation[2][2]);\n }\n\n // Apply translation if provided\n if (translation) {\n Mat4.setTranslation(\n matrix,\n Vec3.create(translation[0], translation[1], translation[2])\n );\n }\n\n // Update the transform with new rotation and translation\n const update = state\n .build()\n .to(targetTransform.transform.ref)\n .update(\n StateTransforms.Model.TransformStructureConformation,\n (old) => ({\n ...old,\n transform: {\n name: \"matrix\" as const,\n params: {\n data: matrix,\n transpose: false,\n },\n },\n })\n );\n\n await this.plugin.runTask(state.updateTree(update));\n }\n }\n\n getPluginContext() {\n return this.plugin;\n }\n}\n\nexport { Plugin };\n","import { Plugin } from \"./Plugin\";\nimport type { InitialUI } from \"./types\";\n\nconst PLUGIN_GC_TIMEOUT = 30 * 1000; // 30 seconds\n\nclass Manager {\n private static instance: Manager;\n\n private initializatingContainers: Set<HTMLElement>;\n private plugins: Map<HTMLElement, Plugin>;\n private refCount: Map<Plugin, [number, number]>; // [count, lastUsedTimestamp]\n private timer: number | undefined;\n\n private constructor() {\n this.initializatingContainers = new Set();\n this.plugins = new Map();\n this.refCount = new Map();\n this.timer = undefined;\n\n this.initGC();\n }\n\n public static getInstance(): Manager {\n if (!Manager.instance) {\n Manager.instance = new Manager();\n }\n\n return Manager.instance;\n }\n\n cleanup() {\n clearInterval(this.timer);\n }\n\n private initGC() {\n this.timer = setInterval(() => {\n const now = Date.now();\n\n for (const [plugin, lastActive] of this.refCount) {\n if (lastActive[0] === 0 && now - lastActive[1] > PLUGIN_GC_TIMEOUT) {\n plugin.dispose();\n }\n }\n }, 20 * 1000); // Run every 20 seconds\n }\n\n async initPlugin(\n container: HTMLElement,\n initialUI: InitialUI\n ): Promise<Plugin> {\n if (this.plugins.has(container)) {\n // biome-ignore lint/style/noNonNullAssertion: Safe because of has() check\n return this.plugins.get(container)!;\n }\n\n if (container.querySelector(\".msp-plugin\")) {\n for (const [containerElem, plugin] of this.plugins) {\n if (containerElem.contains(container)) {\n return plugin;\n }\n }\n }\n\n if (this.initializatingContainers.has(container)) {\n while (this.initializatingContainers.has(container)) {\n await new Promise((resolve) => setTimeout(resolve, 100));\n }\n\n const plugin = this.plugins.get(container);\n if (!plugin) {\n throw new Error(\"Viewer initialization failed\");\n }\n\n return plugin;\n }\n\n try {\n this.initializatingContainers.add(container);\n\n if (!container.querySelector(\".msp-plugin\")) {\n container.innerHTML = \"\";\n }\n\n const instance = await Plugin.create(container, initialUI);\n this.refCount.set(instance, [1, Date.now()]);\n\n this.plugins.set(container, instance);\n return instance;\n } finally {\n this.initializatingContainers.delete(container);\n }\n }\n\n getPlugin(container: HTMLElement): Plugin | undefined {\n const plugin = this.plugins.get(container);\n\n if (plugin) {\n const ref = this.refCount.get(plugin);\n if (ref) {\n ref[0]++;\n ref[1] = Date.now();\n }\n }\n\n return plugin;\n }\n\n releasePlugin(plugin: Plugin) {\n const ref = this.refCount.get(plugin);\n if (!ref) {\n throw new Error(\"Trying to release a plugin that is not managed\");\n }\n\n ref[0] = Math.max(0, ref[0] - 1);\n ref[1] = Date.now();\n }\n\n disposePlugin(container: HTMLElement) {\n const plugin = this.plugins.get(container);\n\n if (plugin) {\n plugin.dispose();\n this.plugins.delete(container);\n container.innerHTML = \"\";\n }\n }\n}\n\nexport { Manager };\n","import type { Protein } from \"../types\";\n\ntype NormalizedChoppingEntry = {\n label: string;\n showLabel: boolean;\n ranges: { start: number; end: number }[];\n};\n\nfunction normalizeChoppingData(\n chopping?: Protein[\"chopping\"]\n): NormalizedChoppingEntry[] {\n if (!chopping) {\n return [];\n }\n\n return chopping\n .map((entry) => ({\n label: entry.label,\n showLabel: entry.showLabel,\n ranges: entry.ranges\n .map((range) => ({\n start: Math.min(range.start, range.end),\n end: Math.max(range.start, range.end),\n }))\n .filter(\n (range) => Number.isFinite(range.start) && Number.isFinite(range.end)\n ),\n }))\n .filter((entry) => entry.ranges.length > 0);\n}\n\nexport type { NormalizedChoppingEntry };\nexport { normalizeChoppingData };\n","import type { ColorHEX } from \"../types\";\nimport type {\n ComponentExpressionT,\n ComponentSelectorT,\n} from \"molstar/lib/extensions/mvs/tree/mvs/param-types\";\n\ntype RGB = [number, number, number];\ntype ShadeMode = \"lighten\" | \"darken\" | \"base\";\n\nconst SHADE_STEPS: { mode: ShadeMode; factor: number }[] = [\n { mode: \"lighten\", factor: 0.5 },\n { mode: \"lighten\", factor: 0.25 },\n { mode: \"base\", factor: 0 },\n { mode: \"darken\", factor: 0.1 },\n { mode: \"darken\", factor: 0.25 },\n { mode: \"darken\", factor: 0.4 },\n];\n\nconst BASE_COLOR_YELLOW: ColorHEX = \"#FD9D0D\";\nconst BASE_COLOR_BLUE: ColorHEX = \"#0D6EFD\";\nconst BASE_COLOR_GREY: ColorHEX = \"#F0F0F0\";\nconst MULTI_DOMAIN_COLORS: ColorHEX[] = [\n \"#4e79a7\",\n \"#f28e2c\",\n \"#e15759\",\n \"#76b7b2\",\n \"#59a14f\",\n \"#edc949\",\n \"#af7aa1\",\n \"#ff9da7\",\n \"#9c755f\",\n \"#bab0ac\",\n] as ColorHEX[];\nconst MULTI_PROTEIN_OPACITY_MAX = 0.5;\nconst MULTI_PROTEIN_OPACITY_MIN = 0.1;\nconst ALPHAFOLD_CONFIDENCE_COLORS = {\n veryHigh: \"#0053D6\" as ColorHEX,\n confident: \"#65CBF3\" as ColorHEX,\n low: \"#FFDB13\" as ColorHEX,\n veryLow: \"#FF7D45\" as ColorHEX,\n};\n\nfunction normalizeHexColor(hex: ColorHEX): ColorHEX {\n const trimmed = hex.trim();\n const withoutHash = trimmed.startsWith(\"#\") ? trimmed.slice(1) : trimmed;\n if (withoutHash.length !== 3 && withoutHash.length !== 6) {\n throw new Error(\"Only 3 or 6 digit hex colors are supported\");\n }\n\n if (!/^[0-9A-Fa-f]+$/.test(withoutHash)) {\n throw new Error(\"Invalid hex color value\");\n }\n\n const expanded =\n withoutHash.length === 3\n ? withoutHash\n .split(\"\")\n .map((char) => char + char)\n .join(\"\")\n : withoutHash;\n\n return `#${expanded.toUpperCase()}` as ColorHEX;\n}\n\nfunction hexToRgb(hex: ColorHEX): RGB {\n const normalized = normalizeHexColor(hex);\n return [\n parseInt(normalized.slice(1, 3), 16),\n parseInt(normalized.slice(3, 5), 16),\n parseInt(normalized.slice(5, 7), 16),\n ];\n}\n\nfunction rgbToHex([r, g, b]: RGB): ColorHEX {\n const channelToHex = (channel: number) =>\n channel.toString(16).padStart(2, \"0\");\n return `#${channelToHex(r)}${channelToHex(g)}${channelToHex(b)}`.toUpperCase() as ColorHEX;\n}\n\nfunction mixChannel(value: number, target: number, factor: number) {\n return Math.round(value + (target - value) * factor);\n}\n\nfunction lightenColor([r, g, b]: RGB, factor: number): RGB {\n return [\n mixChannel(r, 255, factor),\n mixChannel(g, 255, factor),\n mixChannel(b, 255, factor),\n ];\n}\n\nfunction darkenColor([r, g, b]: RGB, factor: number): RGB {\n return [\n mixChannel(r, 0, factor),\n mixChannel(g, 0, factor),\n mixChannel(b, 0, factor),\n ];\n}\n\nfunction makeShades(color: ColorHEX, count: number): ColorHEX[] {\n if (count < 1) {\n throw new Error(\"Count must be at least 1\");\n }\n\n const baseColor = hexToRgb(color);\n const palette = SHADE_STEPS.map((step) => {\n if (step.mode === \"lighten\") {\n return rgbToHex(lightenColor(baseColor, step.factor));\n }\n\n if (step.mode === \"darken\") {\n return rgbToHex(darkenColor(baseColor, step.factor));\n }\n\n return rgbToHex(baseColor);\n });\n\n const shades: ColorHEX[] = [];\n for (let i = 0; i < count; i++) {\n shades.push(palette[i % palette.length]!);\n }\n\n return shades;\n}\n\nfunction getBaseColor(colors: ColorHEX[], index: number): ColorHEX {\n return colors[index] ?? BASE_COLOR_GREY;\n}\n\nfunction getOpacityForProtein(\n index: number,\n totalProteins: number\n): number | undefined {\n if (totalProteins < 3 || index === 0) {\n return undefined;\n }\n\n const range = MULTI_PROTEIN_OPACITY_MAX - MULTI_PROTEIN_OPACITY_MIN;\n const step = range / (totalProteins - 1);\n return Math.max(\n MULTI_PROTEIN_OPACITY_MIN,\n MULTI_PROTEIN_OPACITY_MAX - (index - 1) * step\n );\n}\n\nfunction applyFlatColor(\n representation: any,\n color: ColorHEX,\n selector?: ComponentSelectorT | ComponentExpressionT | ComponentExpressionT[]\n) {\n const params: {\n color: ColorHEX;\n selector?:\n | ComponentSelectorT\n | ComponentExpressionT\n | ComponentExpressionT[];\n } = { color };\n\n if (selector) {\n params.selector = selector;\n }\n\n representation.color(params);\n}\n\nfunction applyAlphaFoldConfidenceColor(\n struct: any,\n component: any,\n representation: any\n) {\n representation.colorFromSource({\n schema: \"all_atomic\",\n category_name: \"atom_site\",\n field_name: \"B_iso_or_equiv\",\n palette: {\n kind: \"discrete\",\n mode: \"absolute\",\n colors: [\n [ALPHAFOLD_CONFIDENCE_COLORS.veryLow, 0],\n [ALPHAFOLD_CONFIDENCE_COLORS.low, 50],\n [ALPHAFOLD_CONFIDENCE_COLORS.confident, 70],\n [ALPHAFOLD_CONFIDENCE_COLORS.veryHigh, 90],\n ],\n },\n });\n\n component.tooltip({ text: \"pLDDT:\" });\n struct.tooltipFromSource({\n schema: \"all_atomic\",\n category_name: \"atom_site\",\n field_name: \"B_iso_or_equiv\",\n });\n}\n\nfunction inferColors(count: number, domains?: number): ColorHEX[] {\n if (count < 0) {\n throw new Error(\"Count must be non-negative\");\n }\n\n if (count === 0) {\n return [];\n }\n\n if (domains !== undefined) {\n if (domains <= 1) {\n throw new Error(\n \"At least two domains are required to infer domain colors\"\n );\n }\n\n return [\"#FF999C\", \"#C8EAFF\", \"#8D272B\", \"#86AEC6\"];\n }\n\n if (count === 1) {\n return [BASE_COLOR_BLUE];\n }\n\n if (count === 2) {\n return [BASE_COLOR_BLUE, BASE_COLOR_YELLOW];\n }\n\n return [BASE_COLOR_YELLOW, ...Array(count - 1).fill(BASE_COLOR_GREY)];\n}\n\nexport {\n BASE_COLOR_BLUE,\n BASE_COLOR_GREY,\n BASE_COLOR_YELLOW,\n MULTI_DOMAIN_COLORS,\n makeShades,\n getBaseColor,\n getOpacityForProtein,\n applyFlatColor,\n applyAlphaFoldConfidenceColor,\n inferColors,\n};\n","import type { Protein } from \"../types\";\n\nfunction createChainSelector(protein: Protein) {\n if (!protein.chain) {\n return \"all\";\n }\n\n return protein.file\n ? { label_asym_id: protein.chain }\n : { auth_asym_id: protein.chain };\n}\n\nfunction getRepresentationType(protein: Protein, representationType?: string) {\n return representationType ?? protein.representation ?? \"cartoon\";\n}\n\nfunction createRepresentationParams(\n protein: Protein,\n representationType?: string\n) {\n const repType = getRepresentationType(protein, representationType);\n\n if (protein.file) {\n return { size_factor: 1, tubular_helices: false, type: repType };\n }\n\n return { type: repType };\n}\n\nfunction isCartoonLikeRepresentation(repType: string) {\n return repType === \"cartoon\" || repType === \"backbone\";\n}\n\nfunction createDomainSelector(\n protein: Protein,\n seqRange?: { beg_auth_seq_id: number; end_auth_seq_id: number }\n) {\n if (!protein.chain) {\n return seqRange ?? \"all\";\n }\n\n const chainId = protein.file\n ? { label_asym_id: protein.chain }\n : { auth_asym_id: protein.chain };\n\n return seqRange ? { ...chainId, ...seqRange } : chainId;\n}\n\nexport {\n createChainSelector,\n createDomainSelector,\n createRepresentationParams,\n getRepresentationType,\n isCartoonLikeRepresentation,\n};\n","import type { ColorHEX, Protein } from \"../types\";\nimport type { ComponentExpressionT } from \"molstar/lib/extensions/mvs/tree/mvs/param-types\";\nimport {\n applyAlphaFoldConfidenceColor,\n applyFlatColor,\n BASE_COLOR_BLUE,\n BASE_COLOR_GREY,\n BASE_COLOR_YELLOW,\n getBaseColor,\n getOpacityForProtein,\n MULTI_DOMAIN_COLORS,\n} from \"./colors\";\nimport type { NormalizedChoppingEntry } from \"./chopping\";\nimport {\n createChainSelector,\n createDomainSelector,\n createRepresentationParams,\n getRepresentationType,\n isCartoonLikeRepresentation,\n} from \"./selectors\";\n\nconst REST_OPACITY = 0.15;\n\nfunction renderProteinWithoutChopping(\n struct: any,\n protein: Protein,\n proteinIndex: number,\n totalProteins: number,\n colors: ColorHEX[]\n) {\n const selector = createChainSelector(protein);\n const comp = struct.component({ selector });\n const repType = getRepresentationType(protein);\n const repr = comp.representation(\n createRepresentationParams(protein, repType)\n );\n\n if (totalProteins === 1) {\n if (isCartoonLikeRepresentation(repType)) {\n applyAlphaFoldConfidenceColor(struct, comp, repr);\n }\n return;\n }\n\n if (totalProteins >= 3) {\n if (proteinIndex === 0 && isCartoonLikeRepresentation(repType)) {\n applyAlphaFoldConfidenceColor(struct, comp, repr);\n } else {\n const color = getBaseColor(colors, proteinIndex);\n applyFlatColor(repr, color);\n const opacity = getOpacityForProtein(proteinIndex, totalProteins);\n if (opacity !== undefined) {\n repr.opacity({ opacity });\n }\n }\n return;\n }\n\n const color = getBaseColor(colors, proteinIndex);\n applyFlatColor(repr, color);\n\n const opacity = getOpacityForProtein(proteinIndex, totalProteins);\n if (opacity !== undefined && opacity < 1) {\n repr.opacity({ opacity });\n }\n}\n\nfunction renderProteinWithChopping(\n struct: any,\n protein: Protein,\n proteinIndex: number,\n totalProteins: number,\n colors: ColorHEX[],\n choppingEntries: NormalizedChoppingEntry[]\n) {\n if (choppingEntries.length === 0) {\n return;\n }\n\n const selector = createChainSelector(protein);\n const comp = struct.component({ selector });\n const baseRepr = comp.representation(createRepresentationParams(protein));\n\n let backgroundColor: ColorHEX;\n let restOpacity = REST_OPACITY;\n if (totalProteins === 1 && choppingEntries.length >= 2) {\n backgroundColor = BASE_COLOR_GREY;\n restOpacity = 1;\n } else {\n backgroundColor = getBaseColor(colors, proteinIndex);\n }\n\n applyFlatColor(baseRepr, backgroundColor);\n baseRepr.opacity({ opacity: restOpacity });\n\n const useInlineDomainColoring =\n totalProteins === 1 && choppingEntries.length >= 2;\n\n let domainPalette: ColorHEX[];\n\n if (totalProteins === 1 && choppingEntries.length >= 2) {\n domainPalette = choppingEntries.map(\n (_, index) => MULTI_DOMAIN_COLORS[index % MULTI_DOMAIN_COLORS.length]!\n );\n } else if (totalProteins === 2 && choppingEntries.length >= 2) {\n const baseColorForDomains =\n proteinIndex === 0 ? BASE_COLOR_BLUE : BASE_COLOR_YELLOW;\n domainPalette = Array(choppingEntries.length).fill(baseColorForDomains);\n } else if (totalProteins === 2 && choppingEntries.length === 1) {\n domainPalette = [backgroundColor];\n } else {\n domainPalette = Array(choppingEntries.length).fill(BASE_COLOR_BLUE);\n }\n\n if (useInlineDomainColoring) {\n choppingEntries.forEach((entry, entryIndex) => {\n applyDomainColor(baseRepr, protein, entry, domainPalette[entryIndex]!);\n addDomainLabel(struct, protein, entry);\n });\n return;\n }\n\n choppingEntries.forEach((entry, entryIndex) => {\n renderDomainEntry(struct, protein, entry, domainPalette[entryIndex]!);\n });\n}\n\nfunction applyDomainColor(\n representation: any,\n protein: Protein,\n entry: NormalizedChoppingEntry,\n color: ColorHEX\n) {\n if (entry.ranges.length === 0) {\n return;\n }\n\n const selectors = entry.ranges.map<ComponentExpressionT>((range) => {\n const seqRange = {\n beg_auth_seq_id: range.start,\n end_auth_seq_id: range.end,\n };\n return createDomainSelector(protein, seqRange) as ComponentExpressionT;\n });\n\n const selectorParam = selectors.length === 1 ? selectors[0]! : selectors;\n applyFlatColor(representation, color, selectorParam);\n}\n\nfunction renderDomainEntry(\n struct: any,\n protein: Protein,\n entry: NormalizedChoppingEntry,\n color: ColorHEX\n) {\n const reprParams = createRepresentationParams(protein);\n\n entry.ranges.forEach((range) => {\n const seqRange = {\n beg_auth_seq_id: range.start,\n end_auth_seq_id: range.end,\n };\n const selector = createDomainSelector(protein, seqRange);\n const domainComp = struct.component({ selector });\n const domainRepr = domainComp.representation(reprParams);\n applyFlatColor(domainRepr, color);\n });\n\n addDomainLabel(struct, protein, entry);\n}\n\nfunction addDomainLabel(\n struct: any,\n protein: Protein,\n entry: NormalizedChoppingEntry\n) {\n if (!entry.showLabel || entry.ranges.length === 0) {\n return;\n }\n\n const labelRange =\n entry.ranges[Math.floor(entry.ranges.length / 2)] ?? entry.ranges[0]!;\n const labelSelector = createDomainSelector(protein, {\n beg_auth_seq_id: labelRange.start,\n end_auth_seq_id: labelRange.end,\n });\n struct.component({ selector: labelSelector }).label({\n text: entry.label,\n });\n}\n\nexport { renderProteinWithChopping, renderProteinWithoutChopping };\n","import type {\n ColorHEX,\n Matrix3D,\n Matrix3DFlattened,\n ModelSourceUrls,\n Protein,\n Vector3D,\n} from \"../types\";\nimport type { MVSData } from \"molstar/lib/extensions/mvs/mvs-data.d.ts\";\nimport type { Plugin } from \"../Plugin\";\nimport {\n createMVSBuilder,\n Root,\n} from \"molstar/lib/extensions/mvs/tree/mvs/mvs-builder\";\nimport { normalizeChoppingData } from \"./chopping\";\nimport { inferColors } from \"./colors\";\nimport {\n renderProteinWithChopping,\n renderProteinWithoutChopping,\n} from \"./rendering\";\n\nfunction transposeAndFlatten(matrix: Matrix3D): Matrix3DFlattened {\n return matrix[0].flatMap((_, colIndex) =>\n matrix.map((row) => row[colIndex])\n ) as Matrix3DFlattened;\n}\n\nconst DEFAULT_ROTATION: Matrix3D = [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n];\nconst DEFAULT_TRANSLATION: Vector3D = [0, 0, 0];\n\nfunction prepareModelSourceUrl(\n protein: Protein,\n modelSourceUrls: Partial<ModelSourceUrls>,\n plugin?: Plugin\n) {\n const defaultModelSourceUrls = {\n uniProtId: \"https://alphafold.ebi.ac.uk/files\",\n };\n\n let url: string;\n\n if (protein.file) {\n if (!plugin) {\n throw new Error(\n \"Plugin instance is required to create object URL from file\"\n );\n }\n\n url = plugin.createObjectUrlFromFile(protein.file);\n } else if (modelSourceUrls.uniProtId !== undefined) {\n url = modelSourceUrls.uniProtId(protein.uniProtId);\n } else {\n url = `${defaultModelSourceUrls.uniProtId}/AF-${protein.uniProtId}-F1-model_v6.cif`;\n }\n\n return url;\n}\n\nfunction getParseFormat(protein: Protein): \"mmcif\" | \"pdb\" {\n if (!protein.file) {\n return \"mmcif\";\n }\n\n return protein.file.name.endsWith(\".cif\") ||\n protein.file.name.endsWith(\".mmcif\")\n ? \"mmcif\"\n : \"pdb\";\n}\n\nfunction processProtein(\n root: Root,\n protein: Protein,\n proteinIndex: number,\n totalProteins: number,\n colors: ColorHEX[],\n modelSourceUrls: Partial<ModelSourceUrls>,\n plugin?: Plugin\n) {\n const url = prepareModelSourceUrl(protein, modelSourceUrls, plugin);\n const download = root.download({ url });\n\n const parseFormat = getParseFormat(protein);\n const parse = download.parse({ format: parseFormat });\n\n const struct = parse.modelStructure(\n protein.file ? { block_header: null, block_index: 0, model_index: 0 } : {}\n );\n\n struct.transform({\n rotation: transposeAndFlatten(\n protein.superposition?.rotation ?? DEFAULT_ROTATION\n ),\n translation: protein.superposition?.translation ?? DEFAULT_TRANSLATION,\n rotation_center: [0, 0, 0],\n });\n\n const choppingEntries =\n totalProteins >= 3 ? [] : normalizeChoppingData(protein.chopping);\n\n if (choppingEntries.length > 0) {\n renderProteinWithChopping(\n struct,\n protein,\n proteinIndex,\n totalProteins,\n colors,\n choppingEntries\n );\n } else {\n renderProteinWithoutChopping(\n struct,\n protein,\n proteinIndex,\n totalProteins,\n colors\n );\n }\n}\n\nfunction createMVS(\n proteins: Protein[],\n modelSourceUrls: Partial<ModelSourceUrls>,\n plugin?: Plugin\n): MVSData {\n const colors = inferColors(proteins.length);\n\n const root = createMVSBuilder();\n\n for (let i = 0; i < proteins.length; i++) {\n const protein = proteins[i]!;\n processProtein(\n root,\n protein,\n i,\n proteins.length,\n colors,\n modelSourceUrls,\n plugin\n );\n }\n\n return root.getState({\n title: proteins.length > 1 ? \"Protein Comparison\" : \"Protein Visualization\",\n description: `Visualization of ${proteins.length} protein(s)`,\n });\n}\n\nexport { createMVS };\n","\"use client\";\n\nimport {\n useEffect,\n useId,\n useRef,\n useState,\n forwardRef,\n useImperativeHandle,\n type CSSProperties,\n} from \"react\";\nimport \"./style.css\";\nimport \"molstar/lib/mol-plugin-ui/skin/light.scss\";\nimport LoaderView from \"./LoaderView\";\nimport ErrorView from \"./ErrorView\";\nimport { Manager } from \"../core/Manager\";\nimport { createMVS } from \"../core/tree\";\nimport type { Plugin as P } from \"../core/Plugin\";\nimport type { Props, ViewerRef } from \"./types\";\n\ntype ViewerState = \"loading\" | \"success\" | \"error\";\n\n/**\n * Viewer\n *\n * React component that embeds a Mol* viewer plugin and exposes a small imperative\n * API via a forwarded ref. The component is responsible for initializing and\n * releasing a shared plugin instance (via Manager), loading structure data (either\n * from raw `proteins` input or from precomputed `mvs`), and exposing convenience\n * controls such as background color and simple animations (spin/rock).\n *\n * Remarks\n * - Exactly one of `proteins` or `mvs` must be provided. Passing both or neither\n * will throw an error during initialization.\n * - The component holds internal loading state: \"loading\" | \"success\" | \"error\".\n * On initialization errors the state becomes \"error\" and the error is logged to\n * the console.\n * - The plugin instance is created/reused via Manager.getInstance() and is\n * released when the component unmounts (or when the effect cleans up).\n * - UI mode `initialUI` toggles whether control chrome is shown; when set to\n * \"minimal\" an additional CSS class (\"no-controls\") is applied to the container.\n *\n * Props\n * @param proteins - Optional raw proteins data used to construct an MVS representation.\n * When provided, the component will call `createMVS(proteins, modelSourceUrls, plugin)`\n * to compute the view state to load into the plugin.\n * @param mvs - Optional precomputed MVS data. If provided, the viewer loads this\n * directly and does not call `createMVS`.\n * @param modelSourceUrls - Optional lookup mapping used by `createMVS` to resolve\n * model source URLs for remote model retrieval when `proteins` is used.\n * Without trailing slashes, e.g. { uniProtId: \"https://api.example.com/protein\" }.\n * @param initialUI - Which initial UI preset to use for the embedded plugin.\n * Typical values: \"standard\" | \"minimal\". Default: \"standard\".\n * @param bgColor - Background color for the viewer (any valid CSS color). Default: \"#ffffff\".\n * @param spin - Whether to enable continuous spin animation. Mutually exclusive with `rock`.\n * @param spinSpeed - Speed multiplier for the spin animation. Default: 0.05.\n * @param rock - Whether to enable rock animation (back-and-forth). Mutually exclusive with `spin`.\n * @param rockSpeed - Speed multiplier for the rock animation. Default: 0.2.\n * @param height - Optional explicit height (in pixels) for the outer wrapper. If omitted,\n * the wrapper will fill available height (\"100%\").\n * @param className - Optional CSS class to apply to the outer wrapper.\n *\n * Forwarded ref (ViewerRef)\n * The component forwards a ref exposing the following async methods:\n * - highlight(domainId: number): Promise<void>\n * Focuses/highlights a domain in the first protein using its choppingData.\n * No-op if plugin or choppingData is not available.\n * - reset(): Promise<void>\n * Resets the plugin's view to its default/original pose.\n * - updateSuperposition(proteinIndex: number, translation?, rotation?): Promise<void>\n * Updates the transform for a loaded structure (protein) without reloading the\n * entire scene. `translation` is an optional [x, y, z] tuple. `rotation` is an\n * optional 3x3 matrix represented as [[r11,r12,r13],[r21,r22,r23],[r31,r32,r33]].\n * This method relies on the Mol* plugin API to update transforms in-place.\n *\n * Behavior & Side Effects\n * - While the component is initializing the plugin and loading data, it renders a\n * LoaderView. If initialization fails, it renders an ErrorView.\n * - When `spin` or `rock` props change (and the component is in \"success\" state),\n * the corresponding plugin animation is enabled with the provided speed. Passing\n * neither results in animations being turned off.\n * - When `bgColor` changes (and the component is in \"success\" state), the plugin's\n * background color is updated.\n * - The container element receives a stable id (useId) and CSS class \"react-molstar\",\n * plus \"no-controls\" when `initialUI === \"minimal\"`. The visualization container's\n * opacity animates between loading/success states.\n *\n * Example\n * const ref = useRef<ViewerRef | null>(null);\n * <Viewer\n * ref={ref}\n * proteins={myProteins}\n * initialUI=\"standard\"\n * bgColor=\"#000\"\n * />\n * // later\n * await ref.current?.highlight(3);\n * await ref.current?.updateSuperposition(1, [10,0,0], [[1,0,0],[0,1,0],[0,0,1]]);\n *\n * See also\n * - Manager: plugin lifecycle management used to acquire/release plugin instances.\n * - createMVS: helper to convert raw protein input into an MVS representation accepted\n * by the plugin.\n */\nconst Viewer = forwardRef<ViewerRef, Props>(function Viewer(\n {\n proteins,\n mvs,\n modelSourceUrls,\n initialUI = \"standard\",\n bgColor = \"#ffffff\",\n spin = false,\n spinSpeed = 0.05,\n rock = false,\n rockSpeed = 0.2,\n height,\n className,\n }: Props,\n ref\n) {\n const containerRef = useRef<HTMLDivElement>(null);\n const pluginRef = useRef<P | null>(null);\n const proteinsRef = 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[number, number, number],\n rotation?: [\n [number, number, number],\n [number, number, number],\n [number, number, number],\n ]\n ) => {\n if (!pluginRef.current) {\n return;\n }\n\n // Use Mol* API directly to update the transform without reloading\n await pluginRef.current.updateStructureTransform(\n proteinIndex,\n translation,\n rotation\n );\n },\n }),\n []\n );\n\n useEffect(() => {\n return () => {\n pluginRef.current = null;\n };\n }, []);\n\n useEffect(() => {\n if (!containerRef.current) {\n return;\n }\n\n if (\n (proteins !== undefined && mvs !== undefined) ||\n (proteins === undefined && mvs === undefined)\n ) {\n throw new Error(\n \"Either `proteins` or `mvs` must be provided, but not both.\"\n );\n }\n\n setState(\"loading\");\n\n let ref: P | undefined;\n\n async function init() {\n const manager = Manager.getInstance();\n\n const el = containerRef.current;\n if (!el) {\n return;\n }\n\n let pl = manager.getPlugin(el);\n if (!pl) {\n pl = await manager.initPlugin(el, initialUI);\n }\n ref = pl;\n pluginRef.current = pl;\n\n try {\n // ensure proteins is defined when mvs is undefined\n if (mvs === undefined && proteins === undefined) {\n throw new Error(\n \"Either `proteins` or `mvs` must be provided, but not both.\"\n );\n }\n\n const proteinsVal = proteins;\n if (mvs === undefined && proteinsVal === undefined) {\n // defensive check, should not happen because of earlier validation\n throw new Error(\"Missing proteins data\");\n }\n\n const proteinsArg = proteinsVal as unknown as Parameters<\n typeof createMVS\n >[0];\n const mvsData =\n mvs ?? createMVS(proteinsArg, modelSourceUrls ?? {}, pl);\n await pl.loadMvs(mvsData);\n } catch (e) {\n // biome-ignore lint/suspicious/noConsole: intentional runtime error logging for viewer init\n console.error(e);\n setState(\"error\");\n return;\n }\n\n setState(\"success\");\n }\n\n init();\n\n return () => {\n if (ref !== undefined) {\n Manager.getInstance().releasePlugin(ref);\n }\n };\n }, [proteins, mvs, 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+ {"version":3,"file":"index.cjs.js","sources":["../node_modules/react/cjs/react-jsx-runtime.production.js","../node_modules/react/cjs/react-jsx-runtime.development.js","../node_modules/react/jsx-runtime.js","../lib/react/LoaderView.tsx","../lib/react/ErrorView.tsx","../lib/core/Plugin.ts","../lib/core/Manager.ts","../lib/core/tree/chopping.ts","../lib/core/tree/colors.ts","../lib/core/tree/selectors.ts","../lib/core/tree/rendering.ts","../lib/core/tree/create-mvs.ts","../lib/react/Viewer.tsx"],"sourcesContent":["/**\n * @license React\n * react-jsx-runtime.production.js\n *\n * Copyright (c) Meta Platforms, Inc. and affiliates.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\n\"use strict\";\nvar REACT_ELEMENT_TYPE = Symbol.for(\"react.transitional.element\"),\n REACT_FRAGMENT_TYPE = Symbol.for(\"react.fragment\");\nfunction jsxProd(type, config, maybeKey) {\n var key = null;\n void 0 !== maybeKey && (key = \"\" + maybeKey);\n void 0 !== config.key && (key = \"\" + config.key);\n if (\"key\" in config) {\n maybeKey = {};\n for (var propName in config)\n \"key\" !== propName && (maybeKey[propName] = config[propName]);\n } else maybeKey = config;\n config = maybeKey.ref;\n return {\n $$typeof: REACT_ELEMENT_TYPE,\n type: type,\n key: key,\n ref: void 0 !== config ? config : null,\n props: maybeKey\n };\n}\nexports.Fragment = REACT_FRAGMENT_TYPE;\nexports.jsx = jsxProd;\nexports.jsxs = jsxProd;\n","/**\n * @license React\n * react-jsx-runtime.development.js\n *\n * Copyright (c) Meta Platforms, Inc. and affiliates.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\n\"use strict\";\n\"production\" !== process.env.NODE_ENV &&\n (function () {\n function getComponentNameFromType(type) {\n if (null == type) return null;\n if (\"function\" === typeof type)\n return type.$$typeof === REACT_CLIENT_REFERENCE\n ? null\n : type.displayName || type.name || null;\n if (\"string\" === typeof type) return type;\n switch (type) {\n case REACT_FRAGMENT_TYPE:\n return \"Fragment\";\n case REACT_PROFILER_TYPE:\n return \"Profiler\";\n case REACT_STRICT_MODE_TYPE:\n return \"StrictMode\";\n case REACT_SUSPENSE_TYPE:\n return \"Suspense\";\n case REACT_SUSPENSE_LIST_TYPE:\n return \"SuspenseList\";\n case REACT_ACTIVITY_TYPE:\n return \"Activity\";\n }\n if (\"object\" === typeof type)\n switch (\n (\"number\" === typeof type.tag &&\n console.error(\n \"Received an unexpected object in getComponentNameFromType(). This is likely a bug in React. Please file an issue.\"\n ),\n type.$$typeof)\n ) {\n case REACT_PORTAL_TYPE:\n return \"Portal\";\n case REACT_CONTEXT_TYPE:\n return type.displayName || \"Context\";\n case REACT_CONSUMER_TYPE:\n return (type._context.displayName || \"Context\") + \".Consumer\";\n case REACT_FORWARD_REF_TYPE:\n var innerType = type.render;\n type = type.displayName;\n type ||\n ((type = innerType.displayName || innerType.name || \"\"),\n (type = \"\" !== type ? \"ForwardRef(\" + type + \")\" : \"ForwardRef\"));\n return type;\n case REACT_MEMO_TYPE:\n return (\n (innerType = type.displayName || null),\n null !== innerType\n ? innerType\n : getComponentNameFromType(type.type) || \"Memo\"\n );\n case REACT_LAZY_TYPE:\n innerType = type._payload;\n type = type._init;\n try {\n return getComponentNameFromType(type(innerType));\n } catch (x) {}\n }\n return null;\n }\n function testStringCoercion(value) {\n return \"\" + value;\n }\n function checkKeyStringCoercion(value) {\n try {\n testStringCoercion(value);\n var JSCompiler_inline_result = !1;\n } catch (e) {\n JSCompiler_inline_result = !0;\n }\n if (JSCompiler_inline_result) {\n JSCompiler_inline_result = console;\n var JSCompiler_temp_const = JSCompiler_inline_result.error;\n var JSCompiler_inline_result$jscomp$0 =\n (\"function\" === typeof Symbol &&\n Symbol.toStringTag &&\n value[Symbol.toStringTag]) ||\n value.constructor.name ||\n \"Object\";\n JSCompiler_temp_const.call(\n JSCompiler_inline_result,\n \"The provided key is an unsupported type %s. This value must be coerced to a string before using it here.\",\n JSCompiler_inline_result$jscomp$0\n );\n return testStringCoercion(value);\n }\n }\n function getTaskName(type) {\n if (type === REACT_FRAGMENT_TYPE) return \"<>\";\n if (\n \"object\" === typeof type &&\n null !== type &&\n type.$$typeof === REACT_LAZY_TYPE\n )\n return \"<...>\";\n try {\n var name = getComponentNameFromType(type);\n return name ? \"<\" + name + \">\" : \"<...>\";\n } catch (x) {\n return \"<...>\";\n }\n }\n function getOwner() {\n var dispatcher = ReactSharedInternals.A;\n return null === dispatcher ? null : dispatcher.getOwner();\n }\n function UnknownOwner() {\n return Error(\"react-stack-top-frame\");\n }\n function hasValidKey(config) {\n if (hasOwnProperty.call(config, \"key\")) {\n var getter = Object.getOwnPropertyDescriptor(config, \"key\").get;\n if (getter && getter.isReactWarning) return !1;\n }\n return void 0 !== config.key;\n }\n function defineKeyPropWarningGetter(props, displayName) {\n function warnAboutAccessingKey() {\n specialPropKeyWarningShown ||\n ((specialPropKeyWarningShown = !0),\n console.error(\n \"%s: `key` is not a prop. Trying to access it will result in `undefined` being returned. If you need to access the same value within the child component, you should pass it as a different prop. (https://react.dev/link/special-props)\",\n displayName\n ));\n }\n warnAboutAccessingKey.isReactWarning = !0;\n Object.defineProperty(props, \"key\", {\n get: warnAboutAccessingKey,\n configurable: !0\n });\n }\n function elementRefGetterWithDeprecationWarning() {\n var componentName = getComponentNameFromType(this.type);\n didWarnAboutElementRef[componentName] ||\n ((didWarnAboutElementRef[componentName] = !0),\n console.error(\n \"Accessing element.ref was removed in React 19. ref is now a regular prop. It will be removed from the JSX Element type in a future release.\"\n ));\n componentName = this.props.ref;\n return void 0 !== componentName ? componentName : null;\n }\n function ReactElement(type, key, props, owner, debugStack, debugTask) {\n var refProp = props.ref;\n type = {\n $$typeof: REACT_ELEMENT_TYPE,\n type: type,\n key: key,\n props: props,\n _owner: owner\n };\n null !== (void 0 !== refProp ? refProp : null)\n ? Object.defineProperty(type, \"ref\", {\n enumerable: !1,\n get: elementRefGetterWithDeprecationWarning\n })\n : Object.defineProperty(type, \"ref\", { enumerable: !1, value: null });\n type._store = {};\n Object.defineProperty(type._store, \"validated\", {\n configurable: !1,\n enumerable: !1,\n writable: !0,\n value: 0\n });\n Object.defineProperty(type, \"_debugInfo\", {\n configurable: !1,\n enumerable: !1,\n writable: !0,\n value: null\n });\n Object.defineProperty(type, \"_debugStack\", {\n configurable: !1,\n enumerable: !1,\n writable: !0,\n value: debugStack\n });\n Object.defineProperty(type, \"_debugTask\", {\n configurable: !1,\n enumerable: !1,\n writable: !0,\n value: debugTask\n });\n Object.freeze && (Object.freeze(type.props), Object.freeze(type));\n return type;\n }\n function jsxDEVImpl(\n type,\n config,\n maybeKey,\n isStaticChildren,\n debugStack,\n debugTask\n ) {\n var children = config.children;\n if (void 0 !== children)\n if (isStaticChildren)\n if (isArrayImpl(children)) {\n for (\n isStaticChildren = 0;\n isStaticChildren < children.length;\n isStaticChildren++\n )\n validateChildKeys(children[isStaticChildren]);\n Object.freeze && Object.freeze(children);\n } else\n console.error(\n \"React.jsx: Static children should always be an array. You are likely explicitly calling React.jsxs or React.jsxDEV. Use the Babel transform instead.\"\n );\n else validateChildKeys(children);\n if (hasOwnProperty.call(config, \"key\")) {\n children = getComponentNameFromType(type);\n var keys = Object.keys(config).filter(function (k) {\n return \"key\" !== k;\n });\n isStaticChildren =\n 0 < keys.length\n ? \"{key: someKey, \" + keys.join(\": ..., \") + \": ...}\"\n : \"{key: someKey}\";\n didWarnAboutKeySpread[children + isStaticChildren] ||\n ((keys =\n 0 < keys.length ? \"{\" + keys.join(\": ..., \") + \": ...}\" : \"{}\"),\n console.error(\n 'A props object containing a \"key\" prop is being spread into JSX:\\n let props = %s;\\n <%s {...props} />\\nReact keys must be passed directly to JSX without using spread:\\n let props = %s;\\n <%s key={someKey} {...props} />',\n isStaticChildren,\n children,\n keys,\n children\n ),\n (didWarnAboutKeySpread[children + isStaticChildren] = !0));\n }\n children = null;\n void 0 !== maybeKey &&\n (checkKeyStringCoercion(maybeKey), (children = \"\" + maybeKey));\n hasValidKey(config) &&\n (checkKeyStringCoercion(config.key), (children = \"\" + config.key));\n if (\"key\" in config) {\n maybeKey = {};\n for (var propName in config)\n \"key\" !== propName && (maybeKey[propName] = config[propName]);\n } else maybeKey = config;\n children &&\n defineKeyPropWarningGetter(\n maybeKey,\n \"function\" === typeof type\n ? type.displayName || type.name || \"Unknown\"\n : type\n );\n return ReactElement(\n type,\n children,\n maybeKey,\n getOwner(),\n debugStack,\n debugTask\n );\n }\n function validateChildKeys(node) {\n isValidElement(node)\n ? node._store && (node._store.validated = 1)\n : \"object\" === typeof node &&\n null !== node &&\n node.$$typeof === REACT_LAZY_TYPE &&\n (\"fulfilled\" === node._payload.status\n ? isValidElement(node._payload.value) &&\n node._payload.value._store &&\n (node._payload.value._store.validated = 1)\n : node._store && (node._store.validated = 1));\n }\n function isValidElement(object) {\n return (\n \"object\" === typeof object &&\n null !== object &&\n object.$$typeof === REACT_ELEMENT_TYPE\n );\n }\n var React = require(\"react\"),\n REACT_ELEMENT_TYPE = Symbol.for(\"react.transitional.element\"),\n REACT_PORTAL_TYPE = Symbol.for(\"react.portal\"),\n REACT_FRAGMENT_TYPE = Symbol.for(\"react.fragment\"),\n REACT_STRICT_MODE_TYPE = Symbol.for(\"react.strict_mode\"),\n REACT_PROFILER_TYPE = Symbol.for(\"react.profiler\"),\n REACT_CONSUMER_TYPE = Symbol.for(\"react.consumer\"),\n REACT_CONTEXT_TYPE = Symbol.for(\"react.context\"),\n REACT_FORWARD_REF_TYPE = Symbol.for(\"react.forward_ref\"),\n REACT_SUSPENSE_TYPE = Symbol.for(\"react.suspense\"),\n REACT_SUSPENSE_LIST_TYPE = Symbol.for(\"react.suspense_list\"),\n REACT_MEMO_TYPE = Symbol.for(\"react.memo\"),\n REACT_LAZY_TYPE = Symbol.for(\"react.lazy\"),\n REACT_ACTIVITY_TYPE = Symbol.for(\"react.activity\"),\n REACT_CLIENT_REFERENCE = Symbol.for(\"react.client.reference\"),\n ReactSharedInternals =\n React.__CLIENT_INTERNALS_DO_NOT_USE_OR_WARN_USERS_THEY_CANNOT_UPGRADE,\n hasOwnProperty = Object.prototype.hasOwnProperty,\n isArrayImpl = Array.isArray,\n createTask = console.createTask\n ? console.createTask\n : function () {\n return null;\n };\n React = {\n react_stack_bottom_frame: function (callStackForError) {\n return callStackForError();\n }\n };\n var specialPropKeyWarningShown;\n var didWarnAboutElementRef = {};\n var unknownOwnerDebugStack = React.react_stack_bottom_frame.bind(\n React,\n UnknownOwner\n )();\n var unknownOwnerDebugTask = createTask(getTaskName(UnknownOwner));\n var didWarnAboutKeySpread = {};\n exports.Fragment = REACT_FRAGMENT_TYPE;\n exports.jsx = function (type, config, maybeKey) {\n var trackActualOwner =\n 1e4 > ReactSharedInternals.recentlyCreatedOwnerStacks++;\n return jsxDEVImpl(\n type,\n config,\n maybeKey,\n !1,\n trackActualOwner\n ? Error(\"react-stack-top-frame\")\n : unknownOwnerDebugStack,\n trackActualOwner ? createTask(getTaskName(type)) : unknownOwnerDebugTask\n );\n };\n exports.jsxs = function (type, config, maybeKey) {\n var trackActualOwner =\n 1e4 > ReactSharedInternals.recentlyCreatedOwnerStacks++;\n return jsxDEVImpl(\n type,\n config,\n maybeKey,\n !0,\n trackActualOwner\n ? Error(\"react-stack-top-frame\")\n : unknownOwnerDebugStack,\n trackActualOwner ? createTask(getTaskName(type)) : unknownOwnerDebugTask\n );\n };\n })();\n","'use strict';\n\nif (process.env.NODE_ENV === 'production') {\n module.exports = require('./cjs/react-jsx-runtime.production.js');\n} else {\n module.exports = require('./cjs/react-jsx-runtime.development.js');\n}\n","export default function LoaderView() {\n return (\n <div\n style={{\n position: \"absolute\",\n top: 0,\n left: 0,\n width: \"100%\",\n height: \"100%\",\n backdropFilter: \"blur(5px)\",\n backgroundColor: \"#0000000A\",\n }}\n >\n <div\n style={{\n position: \"absolute\",\n top: \"50%\",\n left: \"50%\",\n transform: \"translate(-50%, -50%)\",\n display: \"flex\",\n flexDirection: \"column\",\n alignItems: \"center\",\n gap: \"1rem\",\n }}\n >\n <div\n style={{\n width: \"48px\",\n height: \"48px\",\n border: \"6px solid #e5e7eb\",\n borderTopColor: \"#3b82f6\",\n borderRadius: \"50%\",\n animation: \"spin 0.8s linear infinite\",\n }}\n />\n <p\n style={{\n margin: 0,\n fontSize: \"0.875rem\",\n color: \"#6b7280\",\n fontFamily: \"system-ui, -apple-system, sans-serif\",\n }}\n >\n Loading...\n </p>\n <style>\n {`\n @keyframes spin {\n to {\n transform: rotate(360deg);\n }\n }\n `}\n </style>\n </div>\n </div>\n );\n}\n","export default function ErrorView() {\n return (\n <div\n style={{\n position: \"absolute\",\n top: 0,\n left: 0,\n width: \"100%\",\n height: \"100%\",\n backdropFilter: \"blur(5px)\",\n backgroundColor: \"#0000000A\",\n }}\n >\n <div\n style={{\n position: \"absolute\",\n top: \"50%\",\n left: \"50%\",\n transform: \"translate(-50%, -50%)\",\n display: \"flex\",\n flexDirection: \"column\",\n alignItems: \"center\",\n gap: \"0.75rem\",\n padding: \"1.5rem\",\n }}\n >\n <div\n style={{\n width: \"48px\",\n height: \"48px\",\n borderRadius: \"50%\",\n backgroundColor: \"#fef2f2\",\n display: \"flex\",\n alignItems: \"center\",\n justifyContent: \"center\",\n }}\n >\n <svg\n width=\"24\"\n height=\"24\"\n viewBox=\"0 0 24 24\"\n fill=\"none\"\n stroke=\"#ef4444\"\n strokeWidth=\"2\"\n strokeLinecap=\"round\"\n strokeLinejoin=\"round\"\n aria-label=\"Error icon\"\n >\n <title>Error</title>\n <circle cx=\"12\" cy=\"12\" r=\"10\" />\n <line x1=\"15\" y1=\"9\" x2=\"9\" y2=\"15\" />\n <line x1=\"9\" y1=\"9\" x2=\"15\" y2=\"15\" />\n </svg>\n </div>\n <div style={{ textAlign: \"center\" }}>\n <p\n style={{\n margin: 0,\n fontSize: \"0.875rem\",\n fontWeight: 600,\n color: \"#1f2937\",\n fontFamily: \"system-ui, -apple-system, sans-serif\",\n }}\n >\n Error loading viewer\n </p>\n <p\n style={{\n margin: \"0.25rem 0 0 0\",\n fontSize: \"0.75rem\",\n color: \"#6b7280\",\n fontFamily: \"system-ui, -apple-system, sans-serif\",\n }}\n >\n Please try refreshing the page\n </p>\n </div>\n </div>\n </div>\n );\n}\n","import { loadMVSData } from \"molstar/lib/extensions/mvs/components/formats\";\nimport type { MVSData } from \"molstar/lib/extensions/mvs/mvs-data.d.ts\";\nimport type { ColorHEX, Matrix3D, Vector3D } from \"./types\";\nimport { Color } from \"molstar/lib/mol-util/color\";\n\nimport { createPluginUI } from \"molstar/lib/mol-plugin-ui\";\nimport { renderReact18 } from \"molstar/lib/mol-plugin-ui/react18\";\nimport { PluginSpec } from \"molstar/lib/mol-plugin/spec\";\nimport { MolViewSpec } from \"molstar/lib/extensions/mvs/behavior\";\nimport { DefaultPluginUISpec } from \"molstar/lib/mol-plugin-ui/spec\";\nimport type { InitialUI } from \"./types\";\nimport type { PluginUIContext } from \"molstar/lib/mol-plugin-ui/context\";\nimport { Mat4, Vec3 } from \"molstar/lib/mol-math/linear-algebra\";\nimport { PluginStateObject } from \"molstar/lib/mol-plugin-state/objects\";\nimport { Script } from \"molstar/lib/mol-script/script\";\nimport {\n StructureElement,\n StructureSelection,\n} from \"molstar/lib/mol-model/structure\";\nimport { StateTransforms } from \"molstar/lib/mol-plugin-state/transforms\";\n\nclass Plugin {\n private plugin: PluginUIContext;\n private objectUrls: Set<string>;\n private labelsVisible: boolean = true;\n private storedLabels: Array<{\n parentRef: string;\n transform: any;\n }> = [];\n\n constructor(plugin: PluginUIContext) {\n this.plugin = plugin;\n this.objectUrls = new Set();\n }\n\n /**\n * Create a Plugin by instantiating the underlying PluginUI.\n * We use a static async factory because constructors cannot be async.\n */\n static async create(\n container: HTMLElement,\n initialUI: InitialUI\n ): Promise<Plugin> {\n const defaultSpec = DefaultPluginUISpec();\n\n if (!container.querySelector(\".msp-plugin\")) {\n container.innerHTML = \"\";\n }\n\n const plugin = await createPluginUI({\n target: container,\n render: renderReact18,\n spec: {\n actions: defaultSpec.actions ?? [],\n behaviors: [\n ...(initialUI !== \"minimal\" ? defaultSpec.behaviors : []),\n PluginSpec.Behavior(MolViewSpec),\n ],\n animations: [...(defaultSpec.animations || [])],\n layout: {\n initial: {\n showControls: initialUI === \"expanded\",\n controlsDisplay: \"reactive\",\n // isExpanded: false,\n },\n },\n components: {\n ...defaultSpec.components,\n },\n canvas3d: {\n ...defaultSpec.canvas3d,\n camera: {\n ...defaultSpec.canvas3d?.camera,\n helper: {\n axes:\n initialUI === \"minimal\"\n ? {\n name: \"off\",\n params: {},\n }\n : defaultSpec.canvas3d?.camera?.helper?.axes,\n },\n },\n },\n },\n });\n\n return new Plugin(plugin);\n }\n\n dispose() {\n this.plugin.dispose();\n this.cleanupObjectUrls();\n }\n\n cleanupObjectUrls() {\n for (const url of this.objectUrls) {\n try {\n URL.revokeObjectURL(url);\n } catch (_e) {\n // ignore\n }\n\n this.objectUrls.delete(url);\n }\n }\n\n createObjectUrlFromFile(file: File): string {\n const url = URL.createObjectURL(file);\n this.objectUrls.add(url);\n return url;\n }\n\n clear() {\n this.plugin.clear();\n }\n\n async loadMvs(mvs: MVSData) {\n return await loadMVSData(this.plugin, mvs, \"mvsj\");\n }\n\n setBackgroundColor(color: ColorHEX) {\n const hexString = color.replace(\"#\", \"0x\");\n\n this.plugin.canvas3d?.setProps({\n renderer: { backgroundColor: Color.fromHexString(hexString) },\n });\n }\n\n /**\n * Set the visibility of labels by removing or adding them to the state tree.\n * This approach is more reliable than trying to modify the isHidden property.\n */\n async setLabelsVisibility(visible: boolean) {\n // If visibility state is already what we want, do nothing\n if (this.labelsVisible === visible) {\n return;\n }\n\n try {\n const state = this.plugin.state.data;\n\n if (visible) {\n // When turning labels on, re-add them from stored data\n if (this.storedLabels.length > 0) {\n const update = state.build();\n\n for (const storedLabel of this.storedLabels) {\n // Find the parent cell\n const parentCell = state.cells.get(storedLabel.parentRef);\n if (!parentCell) continue;\n\n // Re-apply the stored transform to re-create the label\n update\n .to(storedLabel.parentRef)\n .apply(\n storedLabel.transform.transformer,\n storedLabel.transform.params\n );\n }\n\n await this.plugin.runTask(state.updateTree(update));\n }\n\n this.labelsVisible = true;\n } else {\n // When turning labels off, remove all label nodes from the state tree\n const allObjects = state.selectQ((q) => q.root.subtree());\n\n // Filter for objects that are labels - only check for \"MVS Custom Label\"\n const labels = allObjects.filter((cell) => {\n // Check if the cell has an object\n if (!cell.obj) return false;\n\n // Get label and description\n const label = cell.obj.label || \"\";\n const description = cell.obj.description || \"\";\n\n // Only check for \"MVS Custom Label\"\n return (\n label === \"MVS Custom Label\" || description === \"MVS Custom Label\"\n );\n });\n\n // Store label data before removing\n this.storedLabels = [];\n\n // Remove each label from the state tree\n if (labels.length > 0) {\n const update = state.build();\n\n for (const labelCell of labels) {\n // Get the parent ref (the component this label is attached to)\n const parentRef = labelCell.transform.parent;\n\n // Store the complete transform data for re-adding later\n this.storedLabels.push({\n parentRef,\n transform: {\n transformer: labelCell.transform.transformer,\n params: labelCell.transform.params,\n },\n });\n\n update.delete(labelCell.transform.ref);\n }\n\n await this.plugin.runTask(state.updateTree(update));\n }\n\n this.labelsVisible = false;\n }\n } catch (e) {\n console.error(\"Error setting label visibility:\", e);\n }\n }\n\n setAnimation(type: \"spin\" | \"rock\" | \"off\", speed?: number) {\n if (type === \"off\") {\n this.plugin.canvas3d?.setProps({\n trackball: {\n animate: {\n name: \"off\",\n params: {},\n },\n },\n });\n\n return;\n }\n\n const animationParams =\n type === \"spin\"\n ? {\n speed: speed ?? 0.05,\n }\n : {\n speed: speed ?? 0.2,\n angle: 10,\n };\n\n this.plugin.canvas3d?.setProps({\n trackball: {\n animate: {\n name: type,\n params: animationParams,\n },\n },\n });\n }\n\n async focusOnDomain(\n domainStart: number,\n domainEnd: number,\n proteinIndex: number = 0\n ) {\n const state = this.plugin.state.data;\n\n // Find all structure cells in the state tree\n const structures = state.selectQ((q) =>\n q.rootsOfType(PluginStateObject.Molecule.Structure)\n );\n\n if (structures.length === 0 || proteinIndex >= structures.length) {\n return;\n }\n\n // Use the specified structure for focusing\n const structureCell = structures[proteinIndex];\n if (!structureCell?.obj) {\n return;\n }\n\n const structureData = structureCell.obj.data;\n\n // Build a selection query for the residue range\n const selection = Script.getStructureSelection(\n (Q) =>\n Q.struct.generator.atomGroups({\n \"residue-test\": Q.core.rel.inRange([\n Q.struct.atomProperty.macromolecular.auth_seq_id(),\n domainStart,\n domainEnd,\n ]),\n }),\n structureData\n );\n\n const loci = StructureSelection.toLociWithSourceUnits(selection);\n\n // Focus camera on the loci\n if (!StructureElement.Loci.isEmpty(loci)) {\n await this.plugin.managers.camera.focusLoci(loci);\n }\n }\n\n async resetView() {\n // Reset camera to show all structures\n await this.plugin.managers.camera.reset();\n }\n\n async updateStructureTransform(\n structureIndex: number,\n translation?: Vector3D,\n rotation?: Matrix3D\n ) {\n const state = this.plugin.state.data;\n\n // Find all structure cells in the state tree\n const structures = state.selectQ((q) =>\n q.rootsOfType(PluginStateObject.Molecule.Structure)\n );\n\n if (structureIndex >= structures.length) {\n return;\n }\n\n const targetStructure = structures[structureIndex];\n if (!targetStructure) {\n return;\n }\n\n // Find transform nodes in the structure's subtree\n const allCells = state.selectQ((q) => q.root.subtree());\n const transforms = allCells.filter(\n (cell) =>\n cell.transform.transformer ===\n StateTransforms.Model.TransformStructureConformation\n );\n\n // Match transform by structure index (assumes structures and transforms are in same order)\n const targetTransform = transforms[structureIndex];\n\n if (targetTransform) {\n // Create the transformation matrix\n const matrix = Mat4.identity();\n\n // Apply rotation if provided\n if (rotation) {\n // Set rotation part of the matrix (top-left 3x3)\n Mat4.setValue(matrix, 0, 0, rotation[0][0]);\n Mat4.setValue(matrix, 0, 1, rotation[0][1]);\n Mat4.setValue(matrix, 0, 2, rotation[0][2]);\n Mat4.setValue(matrix, 1, 0, rotation[1][0]);\n Mat4.setValue(matrix, 1, 1, rotation[1][1]);\n Mat4.setValue(matrix, 1, 2, rotation[1][2]);\n Mat4.setValue(matrix, 2, 0, rotation[2][0]);\n Mat4.setValue(matrix, 2, 1, rotation[2][1]);\n Mat4.setValue(matrix, 2, 2, rotation[2][2]);\n }\n\n // Apply translation if provided\n if (translation) {\n Mat4.setTranslation(\n matrix,\n Vec3.create(translation[0], translation[1], translation[2])\n );\n }\n\n // Update the transform with new rotation and translation\n const update = state\n .build()\n .to(targetTransform.transform.ref)\n .update(\n StateTransforms.Model.TransformStructureConformation,\n (old) => ({\n ...old,\n transform: {\n name: \"matrix\" as const,\n params: {\n data: matrix,\n transpose: false,\n },\n },\n })\n );\n\n await this.plugin.runTask(state.updateTree(update));\n }\n }\n\n getPluginContext() {\n return this.plugin;\n }\n}\n\nexport { Plugin };\n","import { Plugin } from \"./Plugin\";\nimport type { InitialUI } from \"./types\";\n\nconst PLUGIN_GC_TIMEOUT = 30 * 1000; // 30 seconds\n\nclass Manager {\n private static instance: Manager;\n\n private initializatingContainers: Set<HTMLElement>;\n private plugins: Map<HTMLElement, Plugin>;\n private refCount: Map<Plugin, [number, number]>; // [count, lastUsedTimestamp]\n private timer: number | undefined;\n\n private constructor() {\n this.initializatingContainers = new Set();\n this.plugins = new Map();\n this.refCount = new Map();\n this.timer = undefined;\n\n this.initGC();\n }\n\n public static getInstance(): Manager {\n if (!Manager.instance) {\n Manager.instance = new Manager();\n }\n\n return Manager.instance;\n }\n\n cleanup() {\n clearInterval(this.timer);\n }\n\n private initGC() {\n this.timer = setInterval(() => {\n const now = Date.now();\n\n for (const [plugin, lastActive] of this.refCount) {\n if (lastActive[0] === 0 && now - lastActive[1] > PLUGIN_GC_TIMEOUT) {\n plugin.dispose();\n }\n }\n }, 20 * 1000); // Run every 20 seconds\n }\n\n async initPlugin(\n container: HTMLElement,\n initialUI: InitialUI\n ): Promise<Plugin> {\n if (this.plugins.has(container)) {\n // biome-ignore lint/style/noNonNullAssertion: Safe because of has() check\n return this.plugins.get(container)!;\n }\n\n if (container.querySelector(\".msp-plugin\")) {\n for (const [containerElem, plugin] of this.plugins) {\n if (containerElem.contains(container)) {\n return plugin;\n }\n }\n }\n\n if (this.initializatingContainers.has(container)) {\n while (this.initializatingContainers.has(container)) {\n await new Promise((resolve) => setTimeout(resolve, 100));\n }\n\n const plugin = this.plugins.get(container);\n if (!plugin) {\n throw new Error(\"Viewer initialization failed\");\n }\n\n return plugin;\n }\n\n try {\n this.initializatingContainers.add(container);\n\n if (!container.querySelector(\".msp-plugin\")) {\n container.innerHTML = \"\";\n }\n\n const instance = await Plugin.create(container, initialUI);\n this.refCount.set(instance, [1, Date.now()]);\n\n this.plugins.set(container, instance);\n return instance;\n } finally {\n this.initializatingContainers.delete(container);\n }\n }\n\n getPlugin(container: HTMLElement): Plugin | undefined {\n const plugin = this.plugins.get(container);\n\n if (plugin) {\n const ref = this.refCount.get(plugin);\n if (ref) {\n ref[0]++;\n ref[1] = Date.now();\n }\n }\n\n return plugin;\n }\n\n releasePlugin(plugin: Plugin) {\n const ref = this.refCount.get(plugin);\n if (!ref) {\n throw new Error(\"Trying to release a plugin that is not managed\");\n }\n\n ref[0] = Math.max(0, ref[0] - 1);\n ref[1] = Date.now();\n }\n\n disposePlugin(container: HTMLElement) {\n const plugin = this.plugins.get(container);\n\n if (plugin) {\n plugin.dispose();\n this.plugins.delete(container);\n container.innerHTML = \"\";\n }\n }\n}\n\nexport { Manager };\n","import type { Protein } from \"../types\";\n\ntype NormalizedChoppingEntry = {\n label: string;\n showLabel: boolean;\n ranges: { start: number; end: number }[];\n};\n\nfunction normalizeChoppingData(\n chopping?: Protein[\"chopping\"]\n): NormalizedChoppingEntry[] {\n if (!chopping) {\n return [];\n }\n\n return chopping\n .map((entry) => ({\n label: entry.label,\n showLabel: entry.showLabel ?? true,\n ranges: entry.ranges\n .map((range) => ({\n start: Math.min(range.start, range.end),\n end: Math.max(range.start, range.end),\n }))\n .filter(\n (range) => Number.isFinite(range.start) && Number.isFinite(range.end)\n ),\n }))\n .filter((entry) => entry.ranges.length > 0);\n}\n\nexport type { NormalizedChoppingEntry };\nexport { normalizeChoppingData };\n","import type { ColorHEX } from \"../types\";\nimport type {\n ComponentExpressionT,\n ComponentSelectorT,\n} from \"molstar/lib/extensions/mvs/tree/mvs/param-types\";\n\ntype RGB = [number, number, number];\ntype ShadeMode = \"lighten\" | \"darken\" | \"base\";\n\nconst SHADE_STEPS: { mode: ShadeMode; factor: number }[] = [\n { mode: \"lighten\", factor: 0.5 },\n { mode: \"lighten\", factor: 0.25 },\n { mode: \"base\", factor: 0 },\n { mode: \"darken\", factor: 0.1 },\n { mode: \"darken\", factor: 0.25 },\n { mode: \"darken\", factor: 0.4 },\n];\n\nconst BASE_COLOR_YELLOW: ColorHEX = \"#FD9D0D\";\nconst BASE_COLOR_BLUE: ColorHEX = \"#0D6EFD\";\nconst BASE_COLOR_GREY: ColorHEX = \"#F0F0F0\";\nconst MULTI_DOMAIN_COLORS: ColorHEX[] = [\n \"#4e79a7\",\n \"#f28e2c\",\n \"#e15759\",\n \"#76b7b2\",\n \"#59a14f\",\n \"#edc949\",\n \"#af7aa1\",\n \"#ff9da7\",\n \"#9c755f\",\n \"#bab0ac\",\n] as ColorHEX[];\nconst MULTI_PROTEIN_OPACITY_MAX = 0.5;\nconst MULTI_PROTEIN_OPACITY_MIN = 0.1;\nconst ALPHAFOLD_CONFIDENCE_COLORS = {\n veryHigh: \"#0053D6\" as ColorHEX,\n confident: \"#65CBF3\" as ColorHEX,\n low: \"#FFDB13\" as ColorHEX,\n veryLow: \"#FF7D45\" as ColorHEX,\n};\n\nfunction normalizeHexColor(hex: ColorHEX): ColorHEX {\n const trimmed = hex.trim();\n const withoutHash = trimmed.startsWith(\"#\") ? trimmed.slice(1) : trimmed;\n if (withoutHash.length !== 3 && withoutHash.length !== 6) {\n throw new Error(\"Only 3 or 6 digit hex colors are supported\");\n }\n\n if (!/^[0-9A-Fa-f]+$/.test(withoutHash)) {\n throw new Error(\"Invalid hex color value\");\n }\n\n const expanded =\n withoutHash.length === 3\n ? withoutHash\n .split(\"\")\n .map((char) => char + char)\n .join(\"\")\n : withoutHash;\n\n return `#${expanded.toUpperCase()}` as ColorHEX;\n}\n\nfunction hexToRgb(hex: ColorHEX): RGB {\n const normalized = normalizeHexColor(hex);\n return [\n parseInt(normalized.slice(1, 3), 16),\n parseInt(normalized.slice(3, 5), 16),\n parseInt(normalized.slice(5, 7), 16),\n ];\n}\n\nfunction rgbToHex([r, g, b]: RGB): ColorHEX {\n const channelToHex = (channel: number) =>\n channel.toString(16).padStart(2, \"0\");\n return `#${channelToHex(r)}${channelToHex(g)}${channelToHex(b)}`.toUpperCase() as ColorHEX;\n}\n\nfunction mixChannel(value: number, target: number, factor: number) {\n return Math.round(value + (target - value) * factor);\n}\n\nfunction lightenColor([r, g, b]: RGB, factor: number): RGB {\n return [\n mixChannel(r, 255, factor),\n mixChannel(g, 255, factor),\n mixChannel(b, 255, factor),\n ];\n}\n\nfunction darkenColor([r, g, b]: RGB, factor: number): RGB {\n return [\n mixChannel(r, 0, factor),\n mixChannel(g, 0, factor),\n mixChannel(b, 0, factor),\n ];\n}\n\nfunction makeShades(color: ColorHEX, count: number): ColorHEX[] {\n if (count < 1) {\n throw new Error(\"Count must be at least 1\");\n }\n\n const baseColor = hexToRgb(color);\n const palette = SHADE_STEPS.map((step) => {\n if (step.mode === \"lighten\") {\n return rgbToHex(lightenColor(baseColor, step.factor));\n }\n\n if (step.mode === \"darken\") {\n return rgbToHex(darkenColor(baseColor, step.factor));\n }\n\n return rgbToHex(baseColor);\n });\n\n const shades: ColorHEX[] = [];\n for (let i = 0; i < count; i++) {\n shades.push(palette[i % palette.length]!);\n }\n\n return shades;\n}\n\nfunction getBaseColor(colors: ColorHEX[], index: number): ColorHEX {\n return colors[index] ?? BASE_COLOR_GREY;\n}\n\nfunction getOpacityForProtein(\n index: number,\n totalProteins: number\n): number | undefined {\n if (totalProteins < 3 || index === 0) {\n return undefined;\n }\n\n const range = MULTI_PROTEIN_OPACITY_MAX - MULTI_PROTEIN_OPACITY_MIN;\n const step = range / (totalProteins - 1);\n return Math.max(\n MULTI_PROTEIN_OPACITY_MIN,\n MULTI_PROTEIN_OPACITY_MAX - (index - 1) * step\n );\n}\n\nfunction applyFlatColor(\n representation: any,\n color: ColorHEX,\n selector?: ComponentSelectorT | ComponentExpressionT | ComponentExpressionT[]\n) {\n const params: {\n color: ColorHEX;\n selector?:\n | ComponentSelectorT\n | ComponentExpressionT\n | ComponentExpressionT[];\n } = { color };\n\n if (selector) {\n params.selector = selector;\n }\n\n representation.color(params);\n}\n\nfunction applyAlphaFoldConfidenceColor(\n struct: any,\n component: any,\n representation: any\n) {\n representation.colorFromSource({\n schema: \"all_atomic\",\n category_name: \"atom_site\",\n field_name: \"B_iso_or_equiv\",\n palette: {\n kind: \"discrete\",\n mode: \"absolute\",\n colors: [\n [ALPHAFOLD_CONFIDENCE_COLORS.veryLow, 0],\n [ALPHAFOLD_CONFIDENCE_COLORS.low, 50],\n [ALPHAFOLD_CONFIDENCE_COLORS.confident, 70],\n [ALPHAFOLD_CONFIDENCE_COLORS.veryHigh, 90],\n ],\n },\n });\n\n component.tooltip({ text: \"pLDDT:\" });\n struct.tooltipFromSource({\n schema: \"all_atomic\",\n category_name: \"atom_site\",\n field_name: \"B_iso_or_equiv\",\n });\n}\n\nfunction inferColors(count: number, domains?: number): ColorHEX[] {\n if (count < 0) {\n throw new Error(\"Count must be non-negative\");\n }\n\n if (count === 0) {\n return [];\n }\n\n if (domains !== undefined) {\n if (domains <= 1) {\n throw new Error(\n \"At least two domains are required to infer domain colors\"\n );\n }\n\n return [\"#FF999C\", \"#C8EAFF\", \"#8D272B\", \"#86AEC6\"];\n }\n\n if (count === 1) {\n return [BASE_COLOR_BLUE];\n }\n\n if (count === 2) {\n return [BASE_COLOR_BLUE, BASE_COLOR_YELLOW];\n }\n\n return [BASE_COLOR_YELLOW, ...Array(count - 1).fill(BASE_COLOR_GREY)];\n}\n\nexport {\n BASE_COLOR_BLUE,\n BASE_COLOR_GREY,\n BASE_COLOR_YELLOW,\n MULTI_DOMAIN_COLORS,\n makeShades,\n getBaseColor,\n getOpacityForProtein,\n applyFlatColor,\n applyAlphaFoldConfidenceColor,\n inferColors,\n};\n","import type { Protein } from \"../types\";\n\nfunction createChainSelector(protein: Protein) {\n if (!protein.chain) {\n return \"all\";\n }\n\n return protein.file\n ? { label_asym_id: protein.chain }\n : { auth_asym_id: protein.chain };\n}\n\nfunction getRepresentationType(protein: Protein, representationType?: string) {\n return representationType ?? protein.representation ?? \"cartoon\";\n}\n\nfunction createRepresentationParams(\n protein: Protein,\n representationType?: string\n) {\n const repType = getRepresentationType(protein, representationType);\n\n if (protein.file) {\n return { size_factor: 1, tubular_helices: false, type: repType };\n }\n\n return { type: repType };\n}\n\nfunction isCartoonLikeRepresentation(repType: string) {\n return repType === \"cartoon\" || repType === \"backbone\";\n}\n\nfunction createDomainSelector(\n protein: Protein,\n seqRange?: { beg_auth_seq_id: number; end_auth_seq_id: number }\n) {\n if (!protein.chain) {\n return seqRange ?? \"all\";\n }\n\n const chainId = protein.file\n ? { label_asym_id: protein.chain }\n : { auth_asym_id: protein.chain };\n\n return seqRange ? { ...chainId, ...seqRange } : chainId;\n}\n\nexport {\n createChainSelector,\n createDomainSelector,\n createRepresentationParams,\n getRepresentationType,\n isCartoonLikeRepresentation,\n};\n","import type { ColorHEX, Protein } from \"../types\";\nimport type { ComponentExpressionT } from \"molstar/lib/extensions/mvs/tree/mvs/param-types\";\nimport {\n applyAlphaFoldConfidenceColor,\n applyFlatColor,\n BASE_COLOR_BLUE,\n BASE_COLOR_GREY,\n BASE_COLOR_YELLOW,\n getBaseColor,\n getOpacityForProtein,\n MULTI_DOMAIN_COLORS,\n} from \"./colors\";\nimport type { NormalizedChoppingEntry } from \"./chopping\";\nimport {\n createChainSelector,\n createDomainSelector,\n createRepresentationParams,\n getRepresentationType,\n isCartoonLikeRepresentation,\n} from \"./selectors\";\n\nconst REST_OPACITY = 0.15;\n\nfunction renderProteinWithoutChopping(\n struct: any,\n protein: Protein,\n proteinIndex: number,\n totalProteins: number,\n colors: ColorHEX[]\n) {\n const selector = createChainSelector(protein);\n const comp = struct.component({ selector });\n const repType = getRepresentationType(protein);\n const repr = comp.representation(\n createRepresentationParams(protein, repType)\n );\n\n if (totalProteins === 1) {\n if (isCartoonLikeRepresentation(repType)) {\n applyAlphaFoldConfidenceColor(struct, comp, repr);\n }\n return;\n }\n\n if (totalProteins >= 3) {\n if (proteinIndex === 0 && isCartoonLikeRepresentation(repType)) {\n applyAlphaFoldConfidenceColor(struct, comp, repr);\n } else {\n const color = getBaseColor(colors, proteinIndex);\n applyFlatColor(repr, color);\n const opacity = getOpacityForProtein(proteinIndex, totalProteins);\n if (opacity !== undefined) {\n repr.opacity({ opacity });\n }\n }\n return;\n }\n\n const color = getBaseColor(colors, proteinIndex);\n applyFlatColor(repr, color);\n\n const opacity = getOpacityForProtein(proteinIndex, totalProteins);\n if (opacity !== undefined && opacity < 1) {\n repr.opacity({ opacity });\n }\n}\n\nfunction renderProteinWithChopping(\n struct: any,\n protein: Protein,\n proteinIndex: number,\n totalProteins: number,\n colors: ColorHEX[],\n choppingEntries: NormalizedChoppingEntry[]\n) {\n if (choppingEntries.length === 0) {\n return;\n }\n\n const selector = createChainSelector(protein);\n const comp = struct.component({ selector });\n const baseRepr = comp.representation(createRepresentationParams(protein));\n\n let backgroundColor: ColorHEX;\n let restOpacity = REST_OPACITY;\n if (totalProteins === 1 && choppingEntries.length >= 2) {\n backgroundColor = BASE_COLOR_GREY;\n restOpacity = 1;\n } else {\n backgroundColor = getBaseColor(colors, proteinIndex);\n }\n\n applyFlatColor(baseRepr, backgroundColor);\n baseRepr.opacity({ opacity: restOpacity });\n\n const useInlineDomainColoring =\n totalProteins === 1 && choppingEntries.length >= 2;\n\n let domainPalette: ColorHEX[];\n\n if (totalProteins === 1 && choppingEntries.length >= 2) {\n domainPalette = choppingEntries.map(\n (_, index) => MULTI_DOMAIN_COLORS[index % MULTI_DOMAIN_COLORS.length]!\n );\n } else if (totalProteins === 2 && choppingEntries.length >= 2) {\n const baseColorForDomains =\n proteinIndex === 0 ? BASE_COLOR_BLUE : BASE_COLOR_YELLOW;\n domainPalette = Array(choppingEntries.length).fill(baseColorForDomains);\n } else if (totalProteins === 2 && choppingEntries.length === 1) {\n domainPalette = [backgroundColor];\n } else {\n domainPalette = Array(choppingEntries.length).fill(BASE_COLOR_BLUE);\n }\n\n if (useInlineDomainColoring) {\n choppingEntries.forEach((entry, entryIndex) => {\n applyDomainColor(baseRepr, protein, entry, domainPalette[entryIndex]!);\n addDomainLabel(struct, protein, entry);\n });\n return;\n }\n\n choppingEntries.forEach((entry, entryIndex) => {\n renderDomainEntry(struct, protein, entry, domainPalette[entryIndex]!);\n });\n}\n\nfunction applyDomainColor(\n representation: any,\n protein: Protein,\n entry: NormalizedChoppingEntry,\n color: ColorHEX\n) {\n if (entry.ranges.length === 0) {\n return;\n }\n\n const selectors = entry.ranges.map<ComponentExpressionT>((range) => {\n const seqRange = {\n beg_auth_seq_id: range.start,\n end_auth_seq_id: range.end,\n };\n return createDomainSelector(protein, seqRange) as ComponentExpressionT;\n });\n\n const selectorParam = selectors.length === 1 ? selectors[0]! : selectors;\n applyFlatColor(representation, color, selectorParam);\n}\n\nfunction renderDomainEntry(\n struct: any,\n protein: Protein,\n entry: NormalizedChoppingEntry,\n color: ColorHEX\n) {\n const reprParams = createRepresentationParams(protein);\n\n entry.ranges.forEach((range) => {\n const seqRange = {\n beg_auth_seq_id: range.start,\n end_auth_seq_id: range.end,\n };\n const selector = createDomainSelector(protein, seqRange);\n const domainComp = struct.component({ selector });\n const domainRepr = domainComp.representation(reprParams);\n applyFlatColor(domainRepr, color);\n });\n\n addDomainLabel(struct, protein, entry);\n}\n\nfunction addDomainLabel(\n struct: any,\n protein: Protein,\n entry: NormalizedChoppingEntry\n) {\n if (!entry.showLabel || entry.ranges.length === 0) {\n return;\n }\n\n const labelRange =\n entry.ranges[Math.floor(entry.ranges.length / 2)] ?? entry.ranges[0]!;\n const labelSelector = createDomainSelector(protein, {\n beg_auth_seq_id: labelRange.start,\n end_auth_seq_id: labelRange.end,\n });\n struct.component({ selector: labelSelector }).label({\n text: entry.label,\n });\n}\n\nexport { renderProteinWithChopping, renderProteinWithoutChopping };\n","import type {\n ColorHEX,\n Matrix3D,\n Matrix3DFlattened,\n ModelSourceUrls,\n Protein,\n Vector3D,\n} from \"../types\";\nimport type { MVSData } from \"molstar/lib/extensions/mvs/mvs-data.d.ts\";\nimport type { Plugin } from \"../Plugin\";\nimport {\n createMVSBuilder,\n Root,\n} from \"molstar/lib/extensions/mvs/tree/mvs/mvs-builder\";\nimport { normalizeChoppingData } from \"./chopping\";\nimport { inferColors } from \"./colors\";\nimport {\n renderProteinWithChopping,\n renderProteinWithoutChopping,\n} from \"./rendering\";\n\nfunction transposeAndFlatten(matrix: Matrix3D): Matrix3DFlattened {\n return matrix[0].flatMap((_, colIndex) =>\n matrix.map((row) => row[colIndex])\n ) as Matrix3DFlattened;\n}\n\nconst DEFAULT_ROTATION: Matrix3D = [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n];\nconst DEFAULT_TRANSLATION: Vector3D = [0, 0, 0];\n\nfunction prepareModelSourceUrl(\n protein: Protein,\n modelSourceUrls: Partial<ModelSourceUrls>,\n plugin?: Plugin\n) {\n const defaultModelSourceUrls = {\n uniProtId: \"https://alphafold.ebi.ac.uk/files\",\n };\n\n let url: string;\n\n if (protein.file) {\n if (!plugin) {\n throw new Error(\n \"Plugin instance is required to create object URL from file\"\n );\n }\n\n url = plugin.createObjectUrlFromFile(protein.file);\n } else if (modelSourceUrls.uniProtId !== undefined) {\n url = modelSourceUrls.uniProtId(protein.uniProtId);\n } else {\n url = `${defaultModelSourceUrls.uniProtId}/AF-${protein.uniProtId}-F1-model_v6.cif`;\n }\n\n return url;\n}\n\nfunction getParseFormat(protein: Protein): \"mmcif\" | \"pdb\" {\n if (!protein.file) {\n return \"mmcif\";\n }\n\n return protein.file.name.endsWith(\".cif\") ||\n protein.file.name.endsWith(\".mmcif\")\n ? \"mmcif\"\n : \"pdb\";\n}\n\nfunction processProtein(\n root: Root,\n protein: Protein,\n proteinIndex: number,\n totalProteins: number,\n colors: ColorHEX[],\n modelSourceUrls: Partial<ModelSourceUrls>,\n plugin?: Plugin\n) {\n const url = prepareModelSourceUrl(protein, modelSourceUrls, plugin);\n const download = root.download({ url });\n\n const parseFormat = getParseFormat(protein);\n const parse = download.parse({ format: parseFormat });\n\n const struct = parse.modelStructure(\n protein.file ? { block_header: null, block_index: 0, model_index: 0 } : {}\n );\n\n struct.transform({\n rotation: transposeAndFlatten(\n protein.superposition?.rotation ?? DEFAULT_ROTATION\n ),\n translation: protein.superposition?.translation ?? DEFAULT_TRANSLATION,\n rotation_center: [0, 0, 0],\n });\n\n const choppingEntries =\n totalProteins >= 3 ? [] : normalizeChoppingData(protein.chopping);\n\n if (choppingEntries.length > 0) {\n renderProteinWithChopping(\n struct,\n protein,\n proteinIndex,\n totalProteins,\n colors,\n choppingEntries\n );\n } else {\n renderProteinWithoutChopping(\n struct,\n protein,\n proteinIndex,\n totalProteins,\n colors\n );\n }\n}\n\nfunction createMVS(\n proteins: Protein[],\n modelSourceUrls: Partial<ModelSourceUrls>,\n plugin?: Plugin\n): MVSData {\n const colors = inferColors(proteins.length);\n\n const root = createMVSBuilder();\n\n for (let i = 0; i < proteins.length; i++) {\n const protein = proteins[i]!;\n processProtein(\n root,\n protein,\n i,\n proteins.length,\n colors,\n modelSourceUrls,\n plugin\n );\n }\n\n return root.getState({\n title: proteins.length > 1 ? \"Protein Comparison\" : \"Protein Visualization\",\n description: `Visualization of ${proteins.length} protein(s)`,\n });\n}\n\nexport { createMVS };\n","\"use client\";\n\nimport {\n useEffect,\n useId,\n useRef,\n useState,\n forwardRef,\n useImperativeHandle,\n type CSSProperties,\n} from \"react\";\nimport \"./style.css\";\nimport \"molstar/lib/mol-plugin-ui/skin/light.scss\";\nimport LoaderView from \"./LoaderView\";\nimport ErrorView from \"./ErrorView\";\nimport { Manager } from \"../core/Manager\";\nimport { createMVS } from \"../core/tree\";\nimport type { Plugin as P } from \"../core/Plugin\";\nimport type { Props, ViewerRef } from \"./types\";\n\ntype ViewerState = \"loading\" | \"success\" | \"error\";\n\n/**\n * Viewer\n *\n * React component that embeds a Mol* viewer plugin and exposes a small imperative\n * API via a forwarded ref. The component is responsible for initializing and\n * releasing a shared plugin instance (via Manager), loading structure data (either\n * from raw `proteins` input or from precomputed `mvs`), and exposing convenience\n * controls such as background color, label visibility, and simple animations (spin/rock).\n *\n * Remarks\n * - Exactly one of `proteins` or `mvs` must be provided. Passing both or neither\n * will throw an error during initialization.\n * - The component holds internal loading state: \"loading\" | \"success\" | \"error\".\n * On initialization errors the state becomes \"error\" and the error is logged to\n * the console.\n * - The plugin instance is created/reused via Manager.getInstance() and is\n * released when the component unmounts (or when the effect cleans up).\n * - UI mode `initialUI` toggles whether control chrome is shown; when set to\n * \"minimal\" an additional CSS class (\"no-controls\") is applied to the container.\n *\n * Props\n * @param proteins - Optional raw proteins data used to construct an MVS representation.\n * When provided, the component will call `createMVS(proteins, modelSourceUrls, plugin)`\n * to compute the view state to load into the plugin.\n * @param mvs - Optional precomputed MVS data. If provided, the viewer loads this\n * directly and does not call `createMVS`.\n * @param modelSourceUrls - Optional lookup mapping used by `createMVS` to resolve\n * model source URLs for remote model retrieval when `proteins` is used.\n * Without trailing slashes, e.g. { uniProtId: \"https://api.example.com/protein\" }.\n * @param initialUI - Which initial UI preset to use for the embedded plugin.\n * Typical values: \"standard\" | \"minimal\". Default: \"standard\".\n * @param bgColor - Background color for the viewer (any valid CSS color). Default: \"#ffffff\".\n * @param labels - Whether to show labels in the viewer. Default: true.\n * @param spin - Whether to enable continuous spin animation. Mutually exclusive with `rock`.\n * @param spinSpeed - Speed multiplier for the spin animation. Default: 0.05.\n * @param rock - Whether to enable rock animation (back-and-forth). Mutually exclusive with `spin`.\n * @param rockSpeed - Speed multiplier for the rock animation. Default: 0.2.\n * @param height - Optional explicit height (in pixels) for the outer wrapper. If omitted,\n * the wrapper will fill available height (\"100%\").\n * @param className - Optional CSS class to apply to the outer wrapper.\n *\n * Forwarded ref (ViewerRef)\n * The component forwards a ref exposing the following async methods:\n * - highlight(proteinIndex: number, label: string): Promise<void>\n * Focuses/highlights a domain within the specified protein by matching the label\n * against the protein's chopping data. The domain's first range (start/end) is used\n * to focus the view. No-op if plugin, proteins, or matching domain is not available.\n * - reset(): Promise<void>\n * Resets the plugin's view to its default/original pose.\n * - updateSuperposition(proteinIndex: number, translation?, rotation?): Promise<void>\n * Updates the transform for a loaded structure (protein) without reloading the\n * entire scene. `translation` is an optional [x, y, z] tuple. `rotation` is an\n * optional 3x3 matrix represented as [[r11,r12,r13],[r21,r22,r23],[r31,r32,r33]].\n * This method relies on the Mol* plugin API to update transforms in-place.\n *\n * Behavior & Side Effects\n * - While the component is initializing the plugin and loading data, it renders a\n * LoaderView. If initialization fails, it renders an ErrorView.\n * - When `spin` or `rock` props change (and the component is in \"success\" state),\n * the corresponding plugin animation is enabled with the provided speed. Passing\n * neither results in animations being turned off.\n * - When `bgColor` changes (and the component is in \"success\" state), the plugin's\n * background color is updated.\n * - When `labels` changes (and the component is in \"success\" state), the plugin's\n * label visibility is updated.\n * - The container element receives a stable id (useId) and CSS class \"react-molstar\",\n * plus \"no-controls\" when `initialUI === \"minimal\"`. The visualization container's\n * opacity animates between loading/success states.\n *\n * Example\n * const ref = useRef<ViewerRef | null>(null);\n * <Viewer\n * ref={ref}\n * proteins={myProteins}\n * initialUI=\"standard\"\n * bgColor=\"#000\"\n * labels={true}\n * />\n * // later\n * await ref.current?.highlight(0, \"Domain A\");\n * await ref.current?.updateSuperposition(1, [10,0,0], [[1,0,0],[0,1,0],[0,0,1]]);\n *\n * See also\n * - Manager: plugin lifecycle management used to acquire/release plugin instances.\n * - createMVS: helper to convert raw protein input into an MVS representation accepted\n * by the plugin.\n */\nconst Viewer = forwardRef<ViewerRef, Props>(function Viewer(\n {\n proteins,\n mvs,\n modelSourceUrls,\n initialUI = \"standard\",\n bgColor = \"#ffffff\",\n spin = false,\n spinSpeed = 0.05,\n rock = false,\n rockSpeed = 0.2,\n height,\n className,\n labels = true,\n }: Props,\n ref\n) {\n const containerRef = useRef<HTMLDivElement>(null);\n const pluginRef = useRef<P | null>(null);\n const proteinsRef = useRef<Props[\"proteins\"]>(proteins);\n const [state, setState] = useState<ViewerState>(\"loading\");\n const id = useId();\n\n // Update proteins ref when proteins prop changes\n useEffect(() => {\n proteinsRef.current = proteins;\n }, [proteins]);\n\n // Expose API methods via ref\n useImperativeHandle(\n ref,\n () => ({\n highlight: async (proteinIndex: number, label: string) => {\n if (\n !pluginRef.current ||\n proteinsRef.current === undefined ||\n proteinsRef.current.length <= proteinIndex\n ) {\n return;\n }\n\n const domain = proteinsRef.current[proteinIndex]?.chopping?.find(\n (d) => d.label === label\n );\n const start = domain?.ranges[0]?.start;\n const end = domain?.ranges[0]?.end;\n\n if (start !== undefined && end !== undefined) {\n await pluginRef.current.focusOnDomain(start, end, proteinIndex);\n }\n },\n reset: async () => {\n if (!pluginRef.current) {\n return;\n }\n await pluginRef.current.resetView();\n },\n updateSuperposition: async (\n proteinIndex: number,\n translation?: [number, number, number],\n rotation?: [\n [number, number, number],\n [number, number, number],\n [number, number, number],\n ]\n ) => {\n if (!pluginRef.current) {\n return;\n }\n\n // Use Mol* API directly to update the transform without reloading\n await pluginRef.current.updateStructureTransform(\n proteinIndex,\n translation,\n rotation\n );\n },\n }),\n []\n );\n\n useEffect(() => {\n return () => {\n pluginRef.current = null;\n };\n }, []);\n\n useEffect(() => {\n if (!containerRef.current) {\n return;\n }\n\n if (\n (proteins !== undefined && mvs !== undefined) ||\n (proteins === undefined && mvs === undefined)\n ) {\n throw new Error(\n \"Either `proteins` or `mvs` must be provided, but not both.\"\n );\n }\n\n setState(\"loading\");\n\n let ref: P | undefined;\n\n async function init() {\n const manager = Manager.getInstance();\n\n const el = containerRef.current;\n if (!el) {\n return;\n }\n\n let pl = manager.getPlugin(el);\n if (!pl) {\n pl = await manager.initPlugin(el, initialUI);\n }\n ref = pl;\n pluginRef.current = pl;\n\n try {\n // ensure proteins is defined when mvs is undefined\n if (mvs === undefined && proteins === undefined) {\n throw new Error(\n \"Either `proteins` or `mvs` must be provided, but not both.\"\n );\n }\n\n const proteinsVal = proteins;\n if (mvs === undefined && proteinsVal === undefined) {\n // defensive check, should not happen because of earlier validation\n throw new Error(\"Missing proteins data\");\n }\n\n const proteinsArg = proteinsVal as unknown as Parameters<\n typeof createMVS\n >[0];\n const mvsData =\n mvs ?? createMVS(proteinsArg, modelSourceUrls ?? {}, pl);\n await pl.loadMvs(mvsData);\n } catch (e) {\n // biome-ignore lint/suspicious/noConsole: intentional runtime error logging for viewer init\n console.error(e);\n setState(\"error\");\n return;\n }\n\n setState(\"success\");\n }\n\n init();\n\n return () => {\n if (ref !== undefined) {\n Manager.getInstance().releasePlugin(ref);\n }\n };\n }, [proteins, mvs, modelSourceUrls, initialUI]);\n\n useEffect(() => {\n if (state !== \"success\" || !pluginRef.current) {\n return;\n }\n\n if (spin) {\n pluginRef.current.setAnimation(\"spin\", spinSpeed);\n } else if (rock) {\n pluginRef.current.setAnimation(\"rock\", rockSpeed);\n } else {\n pluginRef.current.setAnimation(\"off\");\n }\n }, [state, spin, rock, spinSpeed, rockSpeed]);\n\n useEffect(() => {\n if (state !== \"success\" || !pluginRef.current) {\n return;\n }\n\n if (bgColor) {\n pluginRef.current.setBackgroundColor(bgColor);\n }\n }, [state, bgColor]);\n\n useEffect(() => {\n if (state !== \"success\" || !pluginRef.current) {\n return;\n }\n\n pluginRef.current.setLabelsVisibility(labels).catch((error) => {\n console.error(\"Error setting label visibility:\", error);\n });\n }, [state, labels]);\n\n const styles: CSSProperties = {\n height: height ? `${height}px` : \"100%\",\n position: \"relative\",\n };\n const 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package/dist/index.es.js CHANGED
@@ -476,6 +476,8 @@ function ErrorView() {
476
476
  class Plugin {
477
477
  plugin;
478
478
  objectUrls;
479
+ labelsVisible = true;
480
+ storedLabels = [];
479
481
  constructor(plugin) {
480
482
  this.plugin = plugin;
481
483
  this.objectUrls = /* @__PURE__ */ new Set();
@@ -555,6 +557,60 @@ class Plugin {
555
557
  renderer: { backgroundColor: Color.fromHexString(hexString) }
556
558
  });
557
559
  }
560
+ /**
561
+ * Set the visibility of labels by removing or adding them to the state tree.
562
+ * This approach is more reliable than trying to modify the isHidden property.
563
+ */
564
+ async setLabelsVisibility(visible) {
565
+ if (this.labelsVisible === visible) {
566
+ return;
567
+ }
568
+ try {
569
+ const state = this.plugin.state.data;
570
+ if (visible) {
571
+ if (this.storedLabels.length > 0) {
572
+ const update = state.build();
573
+ for (const storedLabel of this.storedLabels) {
574
+ const parentCell = state.cells.get(storedLabel.parentRef);
575
+ if (!parentCell) continue;
576
+ update.to(storedLabel.parentRef).apply(
577
+ storedLabel.transform.transformer,
578
+ storedLabel.transform.params
579
+ );
580
+ }
581
+ await this.plugin.runTask(state.updateTree(update));
582
+ }
583
+ this.labelsVisible = true;
584
+ } else {
585
+ const allObjects = state.selectQ((q) => q.root.subtree());
586
+ const labels = allObjects.filter((cell) => {
587
+ if (!cell.obj) return false;
588
+ const label = cell.obj.label || "";
589
+ const description = cell.obj.description || "";
590
+ return label === "MVS Custom Label" || description === "MVS Custom Label";
591
+ });
592
+ this.storedLabels = [];
593
+ if (labels.length > 0) {
594
+ const update = state.build();
595
+ for (const labelCell of labels) {
596
+ const parentRef = labelCell.transform.parent;
597
+ this.storedLabels.push({
598
+ parentRef,
599
+ transform: {
600
+ transformer: labelCell.transform.transformer,
601
+ params: labelCell.transform.params
602
+ }
603
+ });
604
+ update.delete(labelCell.transform.ref);
605
+ }
606
+ await this.plugin.runTask(state.updateTree(update));
607
+ }
608
+ this.labelsVisible = false;
609
+ }
610
+ } catch (e) {
611
+ console.error("Error setting label visibility:", e);
612
+ }
613
+ }
558
614
  setAnimation(type, speed) {
559
615
  if (type === "off") {
560
616
  this.plugin.canvas3d?.setProps({
@@ -582,15 +638,15 @@ class Plugin {
582
638
  }
583
639
  });
584
640
  }
585
- async focusOnDomain(domainStart, domainEnd) {
641
+ async focusOnDomain(domainStart, domainEnd, proteinIndex = 0) {
586
642
  const state = this.plugin.state.data;
587
643
  const structures = state.selectQ(
588
644
  (q) => q.rootsOfType(PluginStateObject.Molecule.Structure)
589
645
  );
590
- if (structures.length === 0) {
646
+ if (structures.length === 0 || proteinIndex >= structures.length) {
591
647
  return;
592
648
  }
593
- const structureCell = structures[0];
649
+ const structureCell = structures[proteinIndex];
594
650
  if (!structureCell?.obj) {
595
651
  return;
596
652
  }
@@ -771,7 +827,7 @@ function normalizeChoppingData(chopping) {
771
827
  }
772
828
  return chopping.map((entry) => ({
773
829
  label: entry.label,
774
- showLabel: entry.showLabel,
830
+ showLabel: entry.showLabel ?? true,
775
831
  ranges: entry.ranges.map((range) => ({
776
832
  start: Math.min(range.start, range.end),
777
833
  end: Math.max(range.start, range.end)
@@ -1107,7 +1163,8 @@ const Viewer = forwardRef(function Viewer2({
1107
1163
  rock = false,
1108
1164
  rockSpeed = 0.2,
1109
1165
  height,
1110
- className
1166
+ className,
1167
+ labels = true
1111
1168
  }, ref) {
1112
1169
  const containerRef = useRef(null);
1113
1170
  const pluginRef = useRef(null);
@@ -1130,7 +1187,7 @@ const Viewer = forwardRef(function Viewer2({
1130
1187
  const start = domain?.ranges[0]?.start;
1131
1188
  const end = domain?.ranges[0]?.end;
1132
1189
  if (start !== void 0 && end !== void 0) {
1133
- await pluginRef.current.focusOnDomain(start, end);
1190
+ await pluginRef.current.focusOnDomain(start, end, proteinIndex);
1134
1191
  }
1135
1192
  },
1136
1193
  reset: async () => {
@@ -1227,6 +1284,14 @@ const Viewer = forwardRef(function Viewer2({
1227
1284
  pluginRef.current.setBackgroundColor(bgColor);
1228
1285
  }
1229
1286
  }, [state, bgColor]);
1287
+ useEffect(() => {
1288
+ if (state !== "success" || !pluginRef.current) {
1289
+ return;
1290
+ }
1291
+ pluginRef.current.setLabelsVisibility(labels).catch((error) => {
1292
+ console.error("Error setting label visibility:", error);
1293
+ });
1294
+ }, [state, labels]);
1230
1295
  const styles = {
1231
1296
  height: height ? `${height}px` : "100%",
1232
1297
  position: "relative"