Merge pull request #1834 from molstar/fix-aromatic-ring-hybridization

Fix aromatic ring detection not accounting for hybridization

.eslintignore

@@ -1,3 +0,0 @@
-node_modules/*
-build/*
-lib/*

.eslintrc.json

@@ -1,120 +0,0 @@
-{
-    "env": {
-        "browser": true,
-        "node": true
-    },
-    "parserOptions": {
-        "ecmaVersion": 2018,
-        "sourceType": "module",
-        "ecmaFeatures": {
-            "impliedStrict": true
-        }
-    },
-    "rules": {
-        "indent": "off",
-        "arrow-parens": [
-            "off",
-            "as-needed"
-        ],
-        "brace-style": "off",
-        "comma-spacing": "off",
-        "space-infix-ops": "error",
-        "comma-dangle": "off",
-        "eqeqeq": [
-            "error",
-            "smart"
-        ],
-        "import/order": "off",
-        "no-eval": "warn",
-        "no-new-wrappers": "warn",
-        "no-trailing-spaces": "error",
-        "no-unsafe-finally": "warn",
-        "no-var": "error",
-        "spaced-comment": "error",
-        "semi": "warn",
-        "no-restricted-syntax": [
-            "error",
-            {
-                "selector": "ExportDefaultDeclaration",
-                "message": "Default exports are not allowed"
-            }
-        ],
-        "no-throw-literal": "error",
-        "key-spacing": "error",
-        "object-curly-spacing": ["error", "always"],
-        "array-bracket-spacing": "error",
-        "space-in-parens": "error",
-        "computed-property-spacing": "error",
-        "prefer-const": ["error", {
-            "destructuring": "all",
-            "ignoreReadBeforeAssign": false
-        }],
-        "space-before-function-paren": "off",
-        "func-call-spacing": "off",
-        "no-multi-spaces": "error",
-        "block-spacing": "error",
-        "keyword-spacing": "off",
-        "space-before-blocks": "error",
-        "semi-spacing": "error"
-    },
-    "overrides": [
-        {
-            "files": ["**/*.ts", "**/*.tsx"],
-            "parser": "@typescript-eslint/parser",
-            "parserOptions": {
-                "project": ["tsconfig.json", "tsconfig.commonjs.json"],
-                "sourceType": "module"
-            },
-            "plugins": [
-                "@typescript-eslint"
-            ],
-            "rules": {
-                "@typescript-eslint/ban-types": "off",
-                "@typescript-eslint/class-name-casing": "off",
-                "@typescript-eslint/indent": [
-                    "error",
-                    4
-                ],
-                "@typescript-eslint/member-delimiter-style": [
-                    "off",
-                    {
-                        "multiline": {
-                            "delimiter": "none",
-                            "requireLast": true
-                        },
-                        "singleline": {
-                            "delimiter": "semi",
-                            "requireLast": false
-                        }
-                    }
-                ],
-                "@typescript-eslint/prefer-namespace-keyword": "warn",
-                "@typescript-eslint/quotes": [
-                    "error",
-                    "single",
-                    {
-                        "avoidEscape": true,
-                        "allowTemplateLiterals": true
-                    }
-                ],
-                "@typescript-eslint/semi": [
-                    "off",
-                    null
-                ],
-                "@typescript-eslint/type-annotation-spacing": "error",
-                "@typescript-eslint/brace-style": [
-                    "error",
-                    "1tbs", { "allowSingleLine": true }
-                ],
-                "@typescript-eslint/comma-spacing": "error",
-                "@typescript-eslint/space-before-function-paren": ["error", {
-                    "anonymous": "always",
-                    "named": "never",
-                    "asyncArrow": "always"
-                }],
-                "@typescript-eslint/func-call-spacing": ["error"],
-                "@typescript-eslint/keyword-spacing": ["error"]
-            }
-        }
-    ]
-}

.git-blame-ignore-revs

@@ -0,0 +1,14 @@
+# added semicolons to linting rules
+fb0634a0f4aab3764b7e6368e38d8dea7615e591
+
+# new linting rules (no default exports, no named tuples)
+6c5224f33e9de20fe9967a82536c269bacf29738
+
+# lint: add space-in-parens rule
+1d21787e7ea1971817813c008351541e4640c261
+
+# lint: add object-curly-spacing rule
+b31302ba3ad4ab7f98aedd500b762be642374ff0
+
+# fix eslint warnings
+3b1513adc0048dc4879f1d70874b3e56aaffd10e

.github/pull_request_template.md

@@ -0,0 +1,11 @@
+<!-- Thank you for contributing to Mol* -->
+
+# Description
+
+
+## Actions
+
+- [ ] Added description of changes to the `[Unreleased]` section of `CHANGELOG.md`
+- [ ] Updated headers of modified files
+- [ ] Added my name to `package.json`'s `contributors`
+- [ ] (Optional but encouraged) Improved documentation in `docs`

.github/workflows/docs.yml

@@ -0,0 +1,62 @@
+name: Build & Deploy Docs
+
+on:
+  push:
+    branches: master
+    paths:
+      - docs/**
+      - ".github/workflows/docs.yml"
+  pull_request:
+    branches: master
+    paths:
+      - docs/**
+      - ".github/workflows/docs.yml"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 👨🏼‍💻 checkout
+        uses: actions/checkout@v4
+
+      - name: 🐍 python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: ⛓️ dependencies
+        run: |
+          pip install mkdocs-material
+      - name: 🔧 build site
+        run: |
+          cd docs
+          mkdocs build
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    if: github.ref == 'refs/heads/master'
+    steps:
+      - name: 👨🏼‍💻 checkout
+        uses: actions/checkout@v4
+
+      - name: 🐍 python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: ⛓️ dependencies
+        run: |
+          pip install mkdocs-material
+      - name: 🔧 build site
+        run: |
+          cd docs
+          mkdocs build
+
+      - name: 🚢 deploy docs
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          deploy_key: ${{ secrets.DOCS_DEPLOY_KEY }}
+          external_repository: molstar/docs
+          publish_branch: gh-pages
+          publish_dir: ./docs/site

.github/workflows/node.yml

@@ -1,6 +1,10 @@
+name: Build
+
 on:
   push:
+    branches: master
   pull_request:
+    branches: master
 
 jobs:
   build:
@@ -9,12 +13,12 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-node@v2
       with:
-        node-version: 17
+        node-version: 20
     - run: npm ci
     - run: sudo apt-get install xvfb
     - name: Lint
       run: npm run lint
     - name: Test
-      run: xvfb-run --auto-servernum npm run jest
+      run: npm install --no-save "gl@^6.0.2" && xvfb-run --auto-servernum npm run jest
     - name: Build
       run: npm run build

.gitignore

@@ -1,5 +1,7 @@
 build/
+deploy/
 lib/
+docs/site/
 
 node_modules/
 debug.log
@@ -10,4 +12,8 @@ tsconfig.commonjs.tsbuildinfo
 *.sublime-workspace
 .idea
 
-.DS_Store
+.DS_Store
+tmp/
+
+dev.pem
+dev-key.pem

.travis.yml

@@ -1,18 +0,0 @@
-language: node_js
-os: linux
-sudo: required
-dist: trusty
-before_install:
-  - sudo apt-get install -y mesa-utils
-  - sudo apt-get install -y xvfb
-  - sudo apt-get install -y libgl1-mesa-dri
-  - sudo apt-get install -y libglapi-mesa
-  - sudo apt-get install -y libosmesa6
-  - sudo apt-get install -y gcc-4.9
-  - sudo apt-get install -y libstdc++6
-  - sudo apt-get install -y libxi-dev
-node_js:
-  - "12"
-  - "10"
-before_script:
-  - export DISPLAY=:99.0; sh -e /etc/init.d/xvfb start

.vscode/extensions.json

@@ -6,7 +6,6 @@
 	"recommendations": [
 		"dbaeumer.vscode-eslint",
 		"firsttris.vscode-jest-runner",
-		"msjsdiag.debugger-for-chrome",
 		"slevesque.shader",
 		"stpn.vscode-graphql",
 		"wayou.vscode-todo-highlight"

.vscode/settings.json

@@ -6,9 +6,4 @@
         "*.vert.ts": "glsl",
         "*.gql.ts": "graphql"
     },
-    "eslint.options": {
-        "overrideConfig": {
-            "ignorePatterns": ["webpack.config.js", "scripts/*"],
-        },
-    }
 }

README.md

@@ -1,6 +1,6 @@
 [![License](http://img.shields.io/badge/license-MIT-blue.svg?style=flat)](./LICENSE)
 [![npm version](https://badge.fury.io/js/molstar.svg)](https://www.npmjs.com/package/molstar)
-[![Build Status](https://travis-ci.org/molstar/molstar.svg?branch=master)](https://travis-ci.org/molstar/molstar)
+[![Build](https://github.com/molstar/molstar/actions/workflows/node.yml/badge.svg)](https://github.com/molstar/molstar/actions/workflows/node.yml)
 [![Gitter](https://badges.gitter.im/molstar/Lobby.svg)](https://gitter.im/molstar/Lobby)
 
 # Mol*
@@ -84,7 +84,16 @@ Wipes the `build` and `lib` directories and `.tsbuildinfo` files.
 
 Runs the cleanup script prior to building the project, forcing a full rebuild of the project.
 
-Use these commands to resolve occassional build failures which may arise after some dependency updates. Once done, `npm run build` should work again. Note that full rebuilds take more time to complete.
+Use these commands to resolve occasional build failures which may arise after some dependency updates. Once done, `npm run build` should work again. Note that full rebuilds take more time to complete.
+
+### Develop with `esbuild`
+
+Experimental support for faster builds with `esbuild`
+- `npm run dev:all` - watch mode for all apps and examples
+- `npm run dev:viewer` - watch mode for viewer
+- `npm run dev:apps` - watch mode for all apps
+- `npm run dev:examples` - watch mode for all examples
+- `npm run dev -- -a <app name 1> <app name 2> -e <example name 1> ...` - watch mode for specified apps/examples. `-a`/`-e` with without any names will build everything.
 
 ### Build for production:
     NODE_ENV=production npm run build
@@ -103,7 +112,6 @@ From the root of the project:
 
 and navigate to `build/viewer`
 
-
 ### Code generation
 **CIF schemas**
 
@@ -118,17 +126,16 @@ and navigate to `build/viewer`
 
 **Ion names**
 
-    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
+    node --max-old-space-size=8192 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
 
+**Saccharide names**
 
-**GraphQL schemas**
-
-    node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
+    node --max-old-space-size=8192 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts
 
 ### Other scripts
 **Create chem comp bond table**
 
-    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
+    node --max-old-space-size=8192 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
 
 **Test model server**
 
@@ -138,7 +145,7 @@ and navigate to `build/viewer`
 
     export NODE_PATH="lib"; node build/state-docs
 
-**Convert any CIF to BinaryCIF**
+**Convert any CIF to BinaryCIF (or vice versa)**
 
     node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
 
@@ -148,6 +155,11 @@ Or
 
     node lib/commonjs/cli/cif2bcif
 
+E.g.
+
+    node lib/commonjs/cli/cif2bcif src.cif out.bcif.gz
+    node lib/commonjs/cli/cif2bcif src.bcif.gz out.cif
+
 ## Development
 
 ### Installation
@@ -159,13 +171,12 @@ If node complains about a missing acorn peer dependency, run the following comma
 
 ### Editor
 
-To get syntax highlighting for shader and graphql files add the following to Visual Code's settings files and make sure relevant extensions are installed in the editor.
+To get syntax highlighting for shader files add the following to Visual Code's settings files and make sure relevant extensions are installed in the editor.
 
     "files.associations": {
         "*.glsl.ts": "glsl",
         "*.frag.ts": "glsl",
-        "*.vert.ts": "glsl",
-        "*.gql.ts": "graphql"
+        "*.vert.ts": "glsl"
     },
 
 ## Publish
@@ -179,9 +190,14 @@ To get syntax highlighting for shader and graphql files add the following to Vis
     npm publish
 
 ## Deploy
+To prepare apps and demos for https://molstar.org deploy, run:
+
     npm run test
-    npm run build
-    node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
+    npm run deploy:local
+
+To commit these changes remotely to the `molstar/molstar.github.io` repo:
+
+    npm run deploy:remote
 
 ## Contributing
 Just open an issue or make a pull request. All contributions are welcome.

breaking-v6-changes.md

@@ -0,0 +1 @@
+- Remove `checkeredCanvasBackground` from `PluginContext` and `PluginContainer`

data/cif-field-names/cif-core-field-names.csv

@@ -14,6 +14,7 @@ chemical.melting_point
 
 chemical_formula.moiety
 chemical_formula.sum
+chemical_formula.iupac
 chemical_formula.weight
 
 atom_type.symbol
@@ -25,6 +26,8 @@ atom_type_scat.source
 
 space_group.crystal_system
 space_group.name_h-m_full
+space_group.name_h-m_alt
+space_group.name_hall
 space_group.it_number
 space_group_symop.operation_xyz
 

data/cif-field-names/mmcif-field-names.csv

@@ -107,6 +107,7 @@ entity.id
 entity.type
 entity.src_method
 entity.pdbx_description
+entity.pdbx_parent_entity_id
 entity.formula_weight
 entity.pdbx_number_of_molecules
 entity.details
@@ -262,6 +263,7 @@ software.version
 struct.entry_id
 struct.title
 struct.pdbx_descriptor
+struct.pdbx_structure_determination_methodology
 
 struct_asym.id
 struct_asym.pdbx_blank_PDB_chainid_flag
@@ -366,18 +368,43 @@ struct_site.details
 
 struct_site_gen.id
 struct_site_gen.site_id
-struct_site_gen.pdbx_num_res
-struct_site_gen.label_comp_id
+struct_site_gen.auth_asym_id
+struct_site_gen.auth_atom_id
+struct_site_gen.auth_comp_id
+struct_site_gen.auth_seq_id
+struct_site_gen.details
+struct_site_gen.label_alt_id
 struct_site_gen.label_asym_id
+struct_site_gen.label_atom_id
+struct_site_gen.label_comp_id
 struct_site_gen.label_seq_id
 struct_site_gen.pdbx_auth_ins_code
-struct_site_gen.auth_comp_id
-struct_site_gen.auth_asym_id
-struct_site_gen.auth_seq_id
-struct_site_gen.label_atom_id
-struct_site_gen.label_alt_id
+struct_site_gen.pdbx_num_res
 struct_site_gen.symmetry
-struct_site_gen.details
+
+struct_site_keywords.site_id
+struct_site_keywords.text
+
+struct_mon_prot_cis.pdbx_id
+struct_mon_prot_cis.auth_asym_id
+struct_mon_prot_cis.auth_comp_id
+struct_mon_prot_cis.auth_seq_id
+struct_mon_prot_cis.label_alt_id
+struct_mon_prot_cis.label_asym_id
+struct_mon_prot_cis.label_comp_id
+struct_mon_prot_cis.label_seq_id
+struct_mon_prot_cis.pdbx_PDB_ins_code
+struct_mon_prot_cis.pdbx_PDB_ins_code_2
+struct_mon_prot_cis.pdbx_PDB_model_num
+struct_mon_prot_cis.pdbx_auth_asym_id_2
+struct_mon_prot_cis.pdbx_auth_comp_id_2
+struct_mon_prot_cis.pdbx_auth_ins_code
+struct_mon_prot_cis.pdbx_auth_ins_code_2
+struct_mon_prot_cis.pdbx_auth_seq_id_2
+struct_mon_prot_cis.pdbx_label_asym_id_2
+struct_mon_prot_cis.pdbx_label_comp_id_2
+struct_mon_prot_cis.pdbx_label_seq_id_2
+struct_mon_prot_cis.pdbx_omega_angle
 
 symmetry.entry_id
 symmetry.cell_setting
@@ -849,6 +876,17 @@ ma_qa_metric_local.metric_value
 ma_qa_metric_local.model_id
 ma_qa_metric_local.ordinal_id
 
+ma_qa_metric_local_pairwise.ordinal_id
+ma_qa_metric_local_pairwise.model_id
+ma_qa_metric_local_pairwise.label_asym_id_1
+ma_qa_metric_local_pairwise.label_comp_id_1
+ma_qa_metric_local_pairwise.label_seq_id_1
+ma_qa_metric_local_pairwise.label_asym_id_2
+ma_qa_metric_local_pairwise.label_comp_id_2
+ma_qa_metric_local_pairwise.label_seq_id_2
+ma_qa_metric_local_pairwise.metric_id
+ma_qa_metric_local_pairwise.metric_value
+
 ma_software_group.group_id
 ma_software_group.ordinal_id
 ma_software_group.software_id

data/pwa/README.md

@@ -0,0 +1,15 @@
+
+The files in this directory are used for deploying the Mol* Viewer as a PWA (Progressive Web App) at https://molstar.org/viewer/. They may serve as an example for creating your own PWA but wont work as-is. See `/script/deploy.js` for where these files are copied and how they are transformed during deployment.
+
+
+## PWA features
+
+- The Service Worker will cache static resources so the Viewer can be used without internet access. This works without installing, i.e., also in Firefox.
+- Once installed, file types listed in the Manifest can be opened from, e.g., the Windows File Explorer.
+
+
+## Notes for development
+
+In Chrome you can see a list of installed PWAs at chrome://apps/. A right-click opens a menu with an option uninstall.
+
+The Chrome Dev Tools have a section 'Application' to inspect and manage PWA aspects like the Manifest and Service Workers.

data/pwa/manifest.webmanifest

@@ -0,0 +1,39 @@
+{
+    "id": "https://molstar.org/viewer/",
+    "name": "Mol* Viewer",
+    "short_name": "Mol*",
+    "description": "Mol* Viewer: a modern web app for 3D visualization and analysis of large biomolecular structures.",
+    "start_url": "./index.html",
+    "theme_color": "#eeece7",
+    "background_color": "#eeece7",
+    "display": "standalone",
+    "icons": [
+        {
+            "src": "favicon.ico",
+            "sizes": "48x48"
+        },
+        {
+            "src": "logo-144.png",
+            "sizes": "144x144"
+        }
+    ],
+    "file_handlers": [
+        {
+            "action": "./index.html",
+            "accept": {
+                "application/vnd.molstar": [".molx", ".molj"],
+                "text/plain": [
+                    ".mol", ".mol2", ".sdf", ".sd", ".pdb", ".ent", ".pdbqt", ".cif", ".mcif", ".mmcif", ".xyz", ".gro", ".lammpstrj",
+                    ".cub", ".cube", ".dx"
+                ],
+                "application/octet-stream": [
+                    ".bcif",
+                    ".dxbin", ".ccp4", ".mrc", ".map", ".dsn6", ".brix"
+                ]
+            }
+        }
+    ],
+    "launch_handler": {
+        "client_mode": ["auto"]
+    }
+}

data/pwa/pwa.js

@@ -0,0 +1,44 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Andy Turner <agdturner@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+window.addEventListener('molstarViewerCreated', e => {
+    const viewer = e.detail.viewer;
+
+    // Handle incoming files
+    if ('launchQueue' in window) {
+        launchQueue.setConsumer((launchParams) => {
+            if (!launchParams.files.length) return;
+
+            const files = [];
+            for (const fileHandle of launchParams.files) {
+                files.push(fileHandle.getFile());
+            }
+
+            Promise.all(files).then((files) => {
+                viewer.loadFiles(files);
+            });
+        });
+    }
+});
+
+// Register Progressive Web App service worker.
+if ('serviceWorker' in navigator) {
+    window.addEventListener('load', function () {
+        navigator.serviceWorker.register('./sw.js')
+            .then(function (registration) {
+                // Registration was successful
+                if (molstar.isDebugMode) {
+                    console.log('ServiceWorker registration successful with scope: ', registration.scope);
+                }
+            }, function (err) {
+                // registration failed :(
+                if (molstar.isDebugMode) {
+                    console.error('ServiceWorker registration failed: ', err);
+                }
+            });
+    });
+}

data/pwa/sw.js

@@ -0,0 +1,60 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Andy Turner <agdturner@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+/** version from package.json, to be filled in during deployment */
+const VERSION = '__MOLSTAR_VERSION__';
+
+const CACHE_NAME = `molstar-viewer-${VERSION}`;
+
+// The static resources that the app needs to function.
+const APP_STATIC_RESOURCES = [
+    'favicon.ico',
+    'index.html',
+    'molstar.css',
+    'molstar.js',
+    'manifest.webmanifest',
+    'logo-144.png',
+    'pwa.js'
+];
+
+async function cacheStaticResources() {
+    const cache = await caches.open(CACHE_NAME);
+    await cache.addAll(APP_STATIC_RESOURCES);
+    await self.skipWaiting(); // Ensures the new service worker takes control immediately.
+}
+
+async function deleteOldCaches() {
+    const keys = await caches.keys();
+    await Promise.all(
+        keys.map((key) => {
+            if (key !== CACHE_NAME) {
+                return caches.delete(key);
+            }
+        }),
+    );
+    await self.clients.claim(); // Ensures the new service worker takes control immediately.
+}
+
+async function respondWithCacheFirst(request) {
+    // Try to match the request with the cache
+    const cachedResponse = await caches.match(request);
+    return cachedResponse || fetch(request);
+}
+
+self.addEventListener('install', (event) => {
+    // console.log(`Service Worker version ${VERSION} installed.`);
+    event.waitUntil(cacheStaticResources());
+});
+
+self.addEventListener('activate', (event) => {
+    // console.log(`Service Worker version ${VERSION} activated.`);
+    event.waitUntil(deleteOldCaches());
+});
+
+self.addEventListener('fetch', (event) => {
+    event.respondWith(respondWithCacheFirst(event.request));
+});

docs/README.md

@@ -0,0 +1,11 @@
+# Mol* Developer Documentation
+
+Contributions to the documentations are highly welcome! Please make a pull request with your changes.
+
+Requires Python 3.x to build. From this directory:
+
+```
+pip install mkdocs-material
+mkdocs serve
+```
+

docs/docs/data-access-tools/convert-to-bcif.md

@@ -0,0 +1,41 @@
+# Convert CIF to BinaryCIF
+BinaryCIF is an efficient, binary flavor of the CIF format. See [specification](https://github.com/molstar/BinaryCIF) and [publication](https://doi.org/10.1371/journal.pcbi.1008247) for further details.
+
+This script reads data in CIF format and converts it lossless to a BinaryCIF file that can be read by Mol* or other 
+applications.
+
+## Example
+```sh
+node lib/commonjs/cli/cif2bcif/index.js file.cif file.bcif
+```
+
+## Usage
+| Argument | Description |
+| --- | --- |
+| `src` | Source CIF to convert (can be gzipped) |
+| `out` | Generated BinaryCIF output path |
+| `-c` | Path to optional config file |
+| `-f` | Path to optional filter file |
+
+```sh
+index.js [-h] [-c CONFIG] [-f FILTER] src out
+```
+
+### Config file
+Controls how certain columns will be encoded. This is a JSON array of instructions:
+```ts
+interface EncodingStrategyHint {
+    categoryName: string,
+    columnName: string,
+    encoding: 'pack' | 'rle' | 'delta' | 'delta-rle',
+    precision?: number
+}
+```
+Identify a particular CIF columns by its name and override the encoding by Integer Packing, Run-Length Encoding, Delta 
+Encoding, or Delta & Run-Length Encoding. You can optionally control the precision if dealing with float values.
+
+### Filter file
+Specifies which categories and columns will be written. This is a plain text file, each line represents one entry. 
+You can specify explicitly which categories or columns to include by adding `category_name` or 
+`category_name.field_name`. You can also choose to ignore some categories or columns by adding `!category_name` or 
+`!category_name.field_name`.

docs/docs/data-access-tools/create-ccd-table.md

@@ -0,0 +1,25 @@
+# Create Table from CCD
+The [Chemical Component Dictionary (CCD)](https://www.wwpdb.org/data/ccd) is as an external reference file describing 
+all residue and small molecule components found in PDB entries. The 
+[Protonation Variants Companion Dictionary (PVCD)](https://www.wwpdb.org/data/ccd) enumerates protonation variants of
+canonical amino acids.
+
+This script bundles all `chem_comp_bond` information from the CCD and the PVCD into a single file for later use.
+Optionally, it can also generate a second output file that contains all `chem_comp_atom` information.
+
+## Example
+```sh
+node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
+```
+
+## Usage
+| Argument | Description |
+| --- | --- |
+| `out` | Generated file output path |
+| `--forceDownload`, `-f` | Force download of CCD and PVCD |
+| `--binary`, `-b` | Output as BinaryCIF |
+| `--ccaOut`, `-a` | File output path of optionally generated chem_comp_atom |
+
+```sh
+create-table.js [-h] [--forceDownload] [--binary] [--ccaOut CCAOUT] out
+```

docs/docs/data-access-tools/extract-ccd-ions.md

@@ -0,0 +1,20 @@
+# Extract Ions from CCD
+The [Chemical Component Dictionary (CCD)](https://www.wwpdb.org/data/ccd) is as an external reference file describing 
+all residue and small molecule components found in PDB entries.
+
+This script extracts all ions from the CCD and provides their names as TypeScript set.
+
+## Example
+```sh
+node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
+```
+
+## Usage
+| Argument | Description |
+| --- | --- |
+| `out` | Generated file output path |
+| `--forceDownload`, `-f` | Force download of CCD |
+
+```sh
+create-ions.js [-h] [--forceDownload] out
+```

docs/docs/data-access-tools/model-server.md

@@ -0,0 +1,119 @@
+# Model Server
+
+Provides access to molecular 1D, 2D, and 3D (sub-)structure models of molecules. Substructures are described by the 
+mol-script (MolQL) language. It has the ability to include additional data to mmCIF “on the fly”, e.g. integrate 
+primary PDB archival data from [Chemical Component Dictionary (CCD)](https://www.wwpdb.org/data/ccd), 
+[Protonation Variants Companion Dictionary (PVCD)](https://www.wwpdb.org/data/ccd) and 
+[Biologically Interesting moleculeReference Dictionary (BIRD)](https://www.wwpdb.org/data/bird). 
+
+## Example
+```sh
+node lib/commonjs/servers/model/server --sourceMap pdb-bcif '/opt/data/bcif/${id}.bcif'
+```
+
+## Usage
+| Argument | Description |
+| --- | --- |
+| `--version`, `-v` | Show program's version number and exit. |
+| `--cfg` | JSON config file path. If a property is not specified, cmd line param/OS variable/default value are used. |
+| `--printCfg` | Print current config for validation and exit. |
+| `--cfgTemplate` | Prints default JSON config template to be modified and exit. |
+| `--apiPrefix` | Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries> |
+| `--defaultPort` | Specify the port the server is running on |
+| `--cacheMaxSizeInBytes` | Read structures are cached, this specifies the cache size, 0 for off. |
+| `--cacheEntryTimeoutMs` | Specify in ms how long to keep entries in cache. |
+| `--requestTimeoutMs` | The maximum number of ms the server spends on a request. |
+| `--queryTimeoutMs` | The maximum time the server dedicates to executing a query in ms. Does not include the time it takes to read and export the data. |
+| `--shutdownTimeoutMinutes` | Server will shut down after this amount of minutes, 0 for off. |
+| `--shutdownTimeoutVarianceMinutes` | Modifies the shutdown timer by +/- `timeoutVarianceMinutes` (to avoid multiple instances shutting at the same time) |
+| `--maxQueryManyQueries` | Maximum number of queries allowed by the query-many at a time |
+| `--defaultSource` | modifies which 'sourceMap' source to use by default |
+| `--sourceMap` | Map `id`s for a `source` to a file path. Example: `pdb-bcif '../../data/bcif/${id}.bcif'` - JS expressions can be used inside `${}`, e.g. `${id.substr(1, 2)}/${id}.mdb` Can be specified multiple times. The `SOURCE` variable (e.g. `pdb-bcif`) is arbitrary and depends on how you plan to use the server. Supported formats: cif, bcif, cif.gz, bcif.gz |
+| `--sourceMapUrl` | Same as `--sourceMap` but for URL. `--sourceMapUrl src url format` Example: `pdb-cif 'https://www.ebi.ac.uk/pdbe/entry-files/download/${id}_updated.cif' cif` Supported formats: cif, bcif, cif.gz, bcif.gz. Supported protocols: http://, https://, gs:// |
+
+```sh
+node lib/commonjs/servers/model/server [-h] [-v]
+        [--cfg CFG]
+        [--printCfg]
+        [--cfgTemplate]
+        [--apiPrefix PREFIX]
+        [--defaultPort PORT]
+        [--cacheMaxSizeInBytes CACHE_SIZE]
+        [--cacheEntryTimeoutMs CACHE_TIMEOUT]
+        [--requestTimeoutMs REQUEST_TIMEOUT]
+        [--queryTimeoutMs QUERY_TIMEOUT]
+        [--shutdownTimeoutMinutes TIME]
+        [--shutdownTimeoutVarianceMinutes VARIANCE]
+        [--maxQueryManyQueries QUERY_MANY_LIMIT]
+        [--defaultSource DEFAULT_SOURCE]
+        [--sourceMap SOURCE PATH]
+        [--sourceMapUrl SOURCE PATH SOURCE_MAP_FORMAT]
+```
+
+### Production Use
+In production, it is required to use a service that will keep the server running, such as [forever.js](https://github.com/foreverjs/forever).
+
+### Memory Issues
+Sometimes nodejs might run into problems with memory. This is usually resolved by adding the ``--max-old-space-size=8192`` parameter.
+
+### Preprocessor Example
+The preprocessor application allows addiing custom data to CIF files and/or 
+[convert CIF to BinaryCIF](./convert-to-bcif.md).
+```sh
+node lib/commonjs/servers/model/preprocess
+```
+
+### Preprocessor Usage
+| Argument | Description |
+| --- | --- |
+| `--input`, `-i` | Input filename |
+| `--outCIF`, `-oc` | Output CIF filename |
+| `--outBCIF`, `-ob` | Output BinaryCIF filename |
+| `--cfg`, `-c` | Config file path |
+| `--folderIn`, `-fin` | Convert folder |
+| `--folderOutCIF`, `-foc` | Convert folder text output |
+| `--folderOutBCIF`, `-fob` | Convert folder binary output |
+| `--folderNumProcesses`, `-fp` | Convert folder number processes |
+
+Example cfg.json:
+```ts                       
+{ 
+    "numProcesses": 1, 
+    "customProperties": { 
+        "sources": [ "wwpdb" ], 
+        "params": { 
+            "wwPDB": { 
+                "chemCompBondTablePath": "./build/data/ccb.bcif"
+            }
+        }
+    }
+}
+```
+
+### Local Mode
+The server can be run in local/file based mode using
+```sh
+node lib/commonjs/servers/model/query
+```
+
+### Custom Properties
+This feature is still in development.
+
+It is possible to provide property descriptors that transform data to internal representation and define how it should 
+be exported into one or mode CIF categories. Examples of this are located in the ``mol-model-props`` module and are 
+linked to the server in the config and ``servers/model/properties``.
+
+## From NPM
+
+```
+npm install --production molstar
+cd ./model-server 
+```
+
+(or ``node node_modules\.bin\model-server`` in Windows).
+
+The NPM package contains all the tools mentioned in the previous sections as "binaries":
+
+- ``model-server``
+- ``model-server-query``
+- ``model-server-preprocess``

docs/docs/data-access-tools/plugin-state-server.md

@@ -0,0 +1,22 @@
+# Plugin State Server
+
+Provides a simple backend for online storing and sharing of Mol* sessions used by 
+[``mol-plugin``](https://github.com/molstar/molstar/tree/master/src/mol-plugin) and 
+[``mol-state``](https://github.com/molstar/molstar/tree/master/src/mol-state) modules.
+
+## Example
+```sh
+node lib/commonjs/servers/plugin-state --workding-folder ~
+```
+
+## Usage
+| Argument | Description |
+| --- | --- |
+| `--working-folder` | Working folder path |
+| `--port` | Server port. Alternatively, use ENV variable PORT. |
+| `--api-prefix` | Server API prefix |
+| `--max-states` | Maximum number of states to save |
+
+```sh
+node lib/commonjs/servers/plugin-state [-h] --working-folder WORKING_FOLDER [--port PORT] [--api-prefix API_PREFIX] [--max-states MAX_STATES]
+```

docs/docs/data-access-tools/volume-server/examples.md

@@ -1,9 +1,9 @@
-Zika Virus
-==========
+# VolumeServer Examples
+
+## Zika Virus
 
 ![Zika Virus](img/zika_downsampled.png)
 
-1TQN
-====
+## 1TQN
 
 ![1tqn](img/1tqn_downsampled.png)

docs/docs/data-access-tools/volume-server/how-it-works.md

@@ -1,5 +1,4 @@
-How it works
-============
+## VolumeServer: How it works
 
 This document provides a high level overview of how the DensityServer works.
 

docs/docs/data-access-tools/volume-server/index.md

@@ -0,0 +1,126 @@
+# VolumeServer
+
+## What is VolumeServer
+
+Provides near-instantaneous access to volumetric data including density maps (for instance, from X-ray crystallography 
+or cryo-electron microscopy experiments), spatial distribution data, output from electrostatic calculations. It works by
+utilizing adaptive downsampling (similar to how Google Earth works). 
+
+It uses the text based CIF and BinaryCIF formats to deliver the data to the client. 
+
+For quick info about the benefits of using the server, check out the [examples](examples.md).
+
+## Installing and Running
+
+Requires nodejs 8+.
+
+### From GitHub
+
+```
+git clone https://github.com/molstar/molstar
+npm install
+```
+
+Afterwards, build the project source:
+
+```
+npm run build:lib
+```
+
+and run the server by 
+
+```
+node lib/commonjs/servers/volume/server
+```
+
+### From NPM
+
+```
+npm install --production molstar
+./volume-server 
+```
+
+(or ``node node_modules\.bin\volume-server`` in Windows).
+
+The NPM package contains all the tools mentioned here as "binaries":
+
+- ``volume-server``
+- ``volume-server-pack``
+- ``volume-server-query``
+
+
+#### Production use
+
+In production it is required to use a service that will keep the server running, such as [forever.js](https://github.com/foreverjs/forever).
+
+
+#### Memory issues
+
+Sometimes nodejs might run into problems with memory. This is usually resolved by adding the ``--max-old-space-size=8192`` parameter.
+
+
+### Preparing the Data
+
+For the server to work, CCP4/MAP (models 0, 1, 2 are supported) input data need to be converted into a custom block format. 
+To achieve this, use the ``pack`` application (``node lib/commonjs/servers/volume/pack`` or ``volume-server-pack`` binary from the NPM package).
+
+### Local Mode
+
+The program  ``lib/commonjs/servers/volume/query`` (``volume-server-query`` in NPM package) can be used to query the data without running a http server.
+
+### Navigating the Source Code
+
+The source code is split into 2 mains parts: ``pack`` and ``server``:
+
+- The ``pack`` part provides the means of converting CCP4 files into the internal block format.
+- The ``server`` includes
+  - ``query``: the main part of the server that handles a query. ``execute.ts`` is the "entry point".
+  - ``algebra``: linear, "coordinate", and "box" algebra provides the means for calculations necessary to concent a user query into a menaningful response.
+  - API wrapper that handles the requests.
+
+## Consuming the Data 
+
+
+The data can be consumed in any (modern) browser using the [ciftools library](https://github.com/molstar/ciftools) (or any other piece of code that can read text or binary CIF).
+
+The [Data Format](./response-data-format.md) document gives a detailed description of the server response format.
+
+As a reference/example of the server usage is available in Mol* ``mol-plugin`` module.
+
+## Hosting the server
+
+### Example
+
+```sh
+node lib/commonjs/servers/volume/server --idMap x-ray '/opt/data/xray/${id}.mdb'
+```
+
+### Usage
+| Argument= | Description |
+| --- | --- |
+| `--cfg` | JSON config file path. If a property is not specified, cmd line param/OS variable/default value are used. |
+| `--printCfg` | Print current config for validation and exit. |
+| `--cfgTemplate` | Prints default JSON config template to be modified and exit. |
+| `--apiPrefix` | Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries> |
+| `--defaultPort` | Specify the port the server is running on |
+| `--shutdownTimeoutMinutes` | Server will shut down after this amount of minutes, 0 for off. |
+| `--shutdownTimeoutVarianceMinutes` | Modifies the shutdown timer by +/- `timeoutVarianceMinutes` (to avoid multiple instances shutting at the same time) |
+| `--idMap` | Map `id`s for a `type` to a file path. Example: `x-ray '../../data/mdb/xray/${id}-ccp4.mdb'` - JS expressions can be used inside `${}`, e.g. `${id.substr(1, 2)}/${id}.mdb` - Can be specified multiple times. - The `TYPE` variable (e.g. `x-ray`) is arbitrary and depends on how you plan to use the server. By default, Mol* Viewer uses `x-ray` and `em`, but any particular use case may vary. - If using URL, it can be http://, https://, gs:// or file:// protocol.|
+| `--maxRequestBlockCount` | Maximum number of blocks that could be read in 1 query. This is somewhat tied to the ``maxOutputSizeInVoxelCountByPrecisionLevel`` in that the `<maximum number of voxel> = maxRequestBlockCount * <block size>^3`. The default block size is 96 which corresponds to 28,311,552 voxels with 32 max blocks. |
+| `--maxFractionalBoxVolume` | The maximum fractional volume of the query box (to prevent queries that are too big). |
+| `--maxOutputSizeInVoxelCountByPrecisionLevel` | What is the (approximate) maximum desired size in voxel count by precision level - Rule of thumb: `<response gzipped size>` in `[<voxel count> / 8, <voxel count> / 4]`. The maximum number of voxels is tied to maxRequestBlockCount. |
+
+```sh
+node lib/commonjs/servers/volume/server [-h] [-v]
+        [--cfg CFG]
+        [--printCfg] 
+        [--cfgTemplate]
+        [--apiPrefix PREFIX]
+        [--defaultPort PORT]
+        [--shutdownTimeoutMinutes TIME]
+        [--shutdownTimeoutVarianceMinutes VARIANCE] 
+        [--idMap TYPE PATH]
+        [--maxRequestBlockCount COUNT] 
+        [--maxFractionalBoxVolume VOLUME]
+        [--maxOutputSizeInVoxelCountByPrecisionLevel LEVEL [LEVEL ...]]
+```

docs/docs/data-access-tools/volume-server/response-data-format.md

@@ -1,10 +1,8 @@
-Data Format
-===========
+# VolumeServer: Response Data Format
 
 This document describes the CIF categories and fields generated by the server.
 
-Query info
-----------
+## Query info
 
 The reponse always contains a data block called ``SERVER`` with this format:
 
@@ -28,8 +26,7 @@ _density_server_result.query_box_b[1]     35.737
 _density_server_result.query_box_b[2]     32.037001 
 ```
 
-Query data
-----------
+## Query data
 
 If the query completed successfully with a non-empty result the response will contain one or more data blocks that correpond to the
 "channels" present in the data (e.g. for x-ray data there will be ``2Fo-Fc`` and ``Fo-Fc``) channels.
@@ -41,6 +38,7 @@ data_2FO-FC
 #
 _volume_data_3d_info.name                         2Fo-Fc 
 ```
+
 ### Axis order
 
 Axis order determines the order of axes of ``origin``, ``dimensions`` and ``sample_count`` fields. It also specifies

docs/docs/extensions/interactions.md

@@ -0,0 +1,4 @@
+# Interactions extension
+
+The Interactions extension enables computing or providing custom interactions between multiple selections/structures.
+For usage, see the [example source code](https://github.com/molstar/molstar/tree/master/src/examples/interactions).

docs/docs/extensions/mvs/index.md

@@ -0,0 +1,3 @@
+# MolViewSpec
+
+Please see the [standalone MolViewSpec documentation](https://molstar.org/mol-view-spec-docs/).

docs/docs/extensions/mvs/integration-examples.html

@@ -0,0 +1,112 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <!-- Replace "latest" by the specific version you want to use, e.g. "4.0.0" -->
+    <script src="https://cdn.jsdelivr.net/npm/molstar@latest/build/viewer/molstar.js"></script>
+    <!-- Replace "latest" by the specific version you want to use, e.g. "4.0.0" -->
+    <link rel="stylesheet" type="text/css" href="https://cdn.jsdelivr.net/npm/molstar@latest/build/viewer/molstar.css" />
+</head>
+
+<body>
+    <h1>Integration of Mol* with MolViewSpec Extension</h1>
+    <p>
+        This page demonstrates several methods to integrate Mol* Viewer in a web page and use MolViewSpec functionality.
+        See the source HTML to see the actual code.
+    </p>
+
+
+    <h2>Method 1: Get MVS view from a server and pass to the viewer</h2>
+    <p>
+        The recommended method is to serve the MVS view files by your server (either as static files or generated by the
+        server on-demand) and call the <code>loadMvsFromUrl</code> method to retrieve and load them.
+        This example uses a MVS view file from the address specified in the <code>sourceUrl</code> variable.
+        If the MVS view file contains relative references, they will be resolved as relative to <code>sourceUrl</code>.
+    </p>
+
+    <div id="viewer1" style="position: relative; width: 500px; height: 500px;"></div>
+    <script>
+        const sourceUrl = 'https://raw.githubusercontent.com/molstar/molstar/master/examples/mvs/1h9t_domain_labels.mvsj';
+        molstar.Viewer.create('viewer1', { layoutIsExpanded: false, layoutShowControls: false })
+            .then(viewer => viewer.loadMvsFromUrl(sourceUrl, 'mvsj'));
+    </script>
+
+
+    <p>
+        A variation of this method uses <code>molstar.PluginExtensions.mvs.loadMVS</code> instead of
+        <code>loadMvsFromUrl</code> and allows replacing the MVS view after it has been loaded.
+    </p>
+
+    <div id="viewer1b" style="position: relative; width: 500px; height: 500px;"></div>
+    <button onclick="loadView1();">View 1</button>
+    <button onclick="loadView2();">View 2</button>
+    <script>
+        let theViewer;
+        function load(viewer, url, replace) {
+            fetch(url)
+                .then(response => response.text())
+                .then(text => molstar.PluginExtensions.mvs.MVSData.fromMVSJ(text))
+                .then(mvsData => molstar.PluginExtensions.mvs.loadMVS(viewer.plugin, mvsData, { sourceUrl: url, sanityChecks: true, replaceExisting: replace }));
+        }
+        function loadView1() {
+            load(theViewer, 'https://raw.githubusercontent.com/molstar/molstar/master/examples/mvs/1cbs.mvsj', true);
+        }
+        function loadView2() {
+            load(theViewer, 'https://raw.githubusercontent.com/molstar/molstar/master/examples/mvs/1cbs-focus.mvsj', true);
+        }
+        molstar.Viewer.create('viewer1b', { layoutIsExpanded: false, layoutShowControls: false })
+            .then(viewer => {
+                theViewer = viewer;
+                loadView1();
+            });
+    </script>
+
+
+    <h2>Method 2: Construct MVS view on frontend and pass to the viewer</h2>
+    <p>
+        Another option is to utilize the MVS builder provided by the extension to build the view on frontend and then
+        pass it to the viewer. This example builds the view in plain JavaScript, directly in a &lt;script&gt; tag in
+        HTML. However, for a better developer experience consider writing the code in TypeScript.
+        If the built MVS view contains relative references, they will be resolved as relative to the URL of this HTML
+        page.
+    </p>
+
+    <div id="viewer2" style="position: relative; width: 500px; height: 500px;"></div>
+    <script>
+        // Build an ad-hoc MVS view
+        const builder = molstar.PluginExtensions.mvs.MVSData.createBuilder();
+        const structure = builder
+            .download({ url: 'https://www.ebi.ac.uk/pdbe/entry-files/1cbs.bcif' })
+            .parse({ format: 'bcif' })
+            .modelStructure({});
+        structure
+            .component({ selector: 'polymer' })
+            .representation({ type: 'cartoon' })
+            .color({ color: 'green' });
+        structure
+            .component({ selector: 'ligand' })
+            .label({ text: 'Retinoic acid' })
+            .focus({})
+            .representation({ type: 'ball_and_stick' })
+            .color({ color: '#cc3399' });
+        const mvsData = builder.getState();
+
+        // Initialize viewer and load MVSJ
+        const mvsj = molstar.PluginExtensions.mvs.MVSData.toMVSJ(mvsData);
+        molstar.Viewer.create('viewer2', { layoutIsExpanded: false, layoutShowControls: false })
+            .then(viewer => viewer.loadMvsData(mvsj, 'mvsj'));
+
+        // // Alternative initialization and loading (avoids encoding and again decoding the data, allows changing the view by using `replaceExisting: true`):
+        // molstar.Viewer.create('viewer2', { layoutIsExpanded: false, layoutShowControls: false })
+        //     .then(viewer => molstar.PluginExtensions.mvs.loadMVS(viewer.plugin, mvsData, { sourceUrl: undefined, sanityChecks: true, replaceExisting: false }));
+    </script>
+
+
+    <p>
+        Again, there is variation with using <code>molstar.PluginExtensions.mvs.loadMVS</code> instead of
+        <code>loadMvsData</code>.
+    </p>
+
+</body>
+
+</html>

docs/docs/extensions/struct-conn.md

@@ -0,0 +1,118 @@
+# wwPDB StructConn extension
+
+The STRUCT_CONN category in the mmCIF file format contains details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on (see more at <https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/struct_conn.html>).
+
+**wwPDB StructConn extension** in Mol* provides functionality to retrieve and visualize these connections.
+
+The extension exposes three functions, located in `src/extensions/wwpdb/struct-conn/index.ts`. 
+
+- `getStructConns` - to retrieve struct_conn records from a loaded structure
+- `inspectStructConn` - to visualize a struct_conn
+- `clearStructConnInspections` - to remove visulizations created by `inspectStructConn`
+
+
+## Example 1
+
+The following example is a minimal HTML using this functionality:
+
+```html
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Mol* Viewer</title>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body style="margin: 0px;">
+        <div style="position: absolute; width: 100%; height: 10%; padding-block: 10px;">
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'disulf1');">disulf1</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'disulf2');">disulf2</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'covale1');">covale1</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'covale2');">covale2</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'covale3');">covale3</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'covale4');">covale4</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'metalc1');">metalc1</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'metalc2');">metalc2</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'metalc3');">metalc3</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'metalc4');">metalc4</button>
+            <button onclick="molstar.PluginExtensions.wwPDBStructConn.clearStructConnInspections(molstarViewer.plugin, '5elb');">CLEAR</button>
+        </div>
+        <div id="app" style="position: absolute; top: 10%; width: 100%; height: 90%;"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            var molstarViewer;
+            molstar.Viewer.create('app', { layoutIsExpanded: false }).then(viewer => {
+                molstarViewer = viewer;
+                viewer.loadPdb('5elb');
+            });
+        </script>
+    </body>
+</html>
+```
+
+The PDB ID (`'5elb'`) can be replaced be `undefined`, in which case the functions will apply to the first loaded structure.
+
+
+## Example 2
+
+This is a more elaborated example, which automatically loads `5elb` (or any PDB entry given in the URL after `?pdb=`), retrieves the list of struct_conns, and creates a button for each struct_conn. 
+
+Be aware that some of the struct_conns may be present in the deposited model but not in the preferred assembly (default view). The presented example will raise a dialog window with error message in such cases, e.g. `disulf6` in entry `5elb`.
+
+```html
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Mol* Viewer - StructConn Extension Demo</title>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <style>
+        body { margin: 0px; }
+        #app { position: absolute; width: 85%; height: 100%; }
+        #controls { position: absolute; right: 0; width: 15%; height: 100%; display: flex; flex-direction: column; overflow-y: scroll; }
+        h1 { text-align: center; margin: 12px; font-weight: bold; font-size: 120%; }
+        button { margin: 4px; margin-top: 0px; }
+    </style>
+    <body>
+        <div id="app"></div>
+        <div id="controls">
+            <h1 id="pdb-id">Loading...</h1>
+            <button onclick="clearInspections();">CLEAR</button>
+        </div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            var pdbId = window.location.search.match(/[?&]pdb=(\w+)/i)?.[1]?.toLowerCase() ?? '5elb';
+            var molstarViewer;
+            function inspect(structConnId) {
+                if (molstarViewer?.plugin) {
+                    molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, pdbId, structConnId).then(nSelectedAtoms => {
+                        if (nSelectedAtoms < 2) alert('Some of the interacting atoms were not found :(\n(maybe not present in the viewed assembly)');
+                    });
+                }
+            }
+            function clearInspections() {
+                if (molstarViewer?.plugin) {
+                    molstar.PluginExtensions.wwPDBStructConn.clearStructConnInspections(molstarViewer.plugin, pdbId);
+                }
+            }
+            molstar.Viewer.create('app', { layoutIsExpanded: false }).then(viewer => {
+                molstarViewer = viewer;
+                return viewer.loadPdb(pdbId);
+            }).then(() => {
+                const structConns = molstar.PluginExtensions.wwPDBStructConn.getStructConns(molstarViewer.plugin, pdbId);
+                const controls = document.getElementById('controls');
+                for (const structConnId in structConns) {
+                    const button = document.createElement('button');
+                    button.innerText = structConnId;
+                    button.addEventListener('click', () => inspect(structConnId));
+                    controls.appendChild(button);
+                };
+                document.getElementById('pdb-id').innerHTML = pdbId;
+            });
+        </script>
+    </body>
+</html>
+```

docs/docs/extensions/tunnels.md

@@ -0,0 +1,118 @@
+# Tunnel Visualization Extension
+This documentation outlines the usage of the Mol* extension for visualizing tunnels in molecular structures. The extension integrates with Mol* to render 3D representations of tunnels using specified data sources and properties.
+
+The extension is a key component in ChannelsDB (https://channelsdb2.biodata.ceitec.cz/), enabling users to visualize tunnels within molecules directly from the database. While it is used with ChannelsDB, users can also input their own data or connect to different databases, ensuring versatility across various research environments.
+
+## Data Types
+The primary data types involved in tunnel visualization are:
+
+### Tunnel
+A Tunnel object contains the actual tunnel data necessary for visualization. It consists of:
+
+- `data`: An array of `Profile` objects that describe the tunnel at various points.
+- `props`: Properties such as the tunnel's type, ID, and optional labels or descriptions.
+
+### Profile
+A `Profile` object in a `Tunnel` holds detailed geometric and physical properties of a tunnel at specific points along its length. These properties include:
+
+- `Charge`: The electric charge at a specific point in the tunnel.
+- `Radius`: The overall radius of the tunnel at this point.
+- `FreeRadius`: The radius of the tunnel not obstructed by any molecular elements.
+- `T`: Temperature factor or a similar property related to the point.
+- `Distance`: Distance along the tunnel's path from the start.
+- `X`, `Y`, `Z`: Coordinates of the point in 3D space.
+
+These profiles are crucial for understanding the physical and chemical environment inside the tunnel, allowing for detailed analysis and visualization.
+
+Example:
+```json
+"Profile": [
+    {
+        "Radius": 1.49,
+        "FreeRadius": 1.49,
+        "T": 0,
+        "Distance": 0,
+        "X": -19.152,
+        "Y": -22.654,
+        "Z": -13.034,
+        "Charge": 0
+    },
+    {
+        "Radius": 1.524,
+        "FreeRadius": 1.524,
+        "T": 0.00625,
+        "Distance": 0.087,
+        "X": -19.162,
+        "Y": -22.596,
+        "Z": -12.969,
+        "Charge": 0
+    },
+    {
+        "Radius": 1.56,
+        "FreeRadius": 1.56,
+        "T": 0.0125,
+        "Distance": 0.174,
+        "X": -19.171,
+        "Y": -22.539,
+        "Z": -12.905,
+        "Charge": 0
+    }
+]
+```
+## Transformers Usage
+The extension uses several transformations to process and visualize tunnel data:
+
+### Tunnels Data Transformer
+- `Purpose`: Converts a collection of Tunnel data into a state object.
+- `Usage`:
+    ```typescript
+    update.toRoot().apply(TunnelsFromRawData, { data: tunnels });
+    ```
+
+### Tunnel Data Provider
+- `Purpose`: Converts single Tunnel data into a state object for individual processing.
+- `Usage`:
+    ```typescript
+    update.toRoot().apply(TunnelFromRawData, {
+        data: {
+            data: tunnel.Profile,
+            props: { id: tunnel.Id, type: tunnel.Type }
+        }
+    });
+    ```
+
+### Tunnel Shape Provider
+- `Purpose`: Provides the shapes for rendering the tunnel based on WebGL context and shape parameters.
+- `Usage`:
+    ```typescript
+    update.apply(TunnelShapeProvider, {
+        webgl,
+    }).apply(StateTransforms.Representation.ShapeRepresentation3D);
+    ```
+
+## Visualization Examples
+To help users understand how to use these transformations in practice, include detailed examples:
+
+### Visualizing Multiple Tunnels
+This example (see `src/extensions/sb-ncbr/tunnels/examples.ts#L19`) demonstrates how to visualize multiple tunnels from a fetched dataset.
+```typescript
+update.toRoot()
+        .apply(TunnelsFromRawData, { data: tunnels })
+        .apply(SelectTunnel)
+        .apply(TunnelShapeProvider, { webgl })
+        .apply(StateTransforms.Representation.ShapeRepresentation3D);
+```
+
+### Visualizing a Single Tunnel
+This example (see `src/extensions/sb-ncbr/tunnels/examples.ts#L46`) shows how to visualize a single tunnel.
+```typescript
+update.toRoot()
+        .apply(TunnelFromRawData, {
+            data: {
+                data: tunnel.Profile,
+                props: { id: tunnel.Id, type: tunnel.Type }
+            }
+        })
+        .apply(TunnelShapeProvider, { webgl })
+        .apply(StateTransforms.Representation.ShapeRepresentation3D);
+```

docs/docs/index.md

@@ -0,0 +1,43 @@
+# Installation
+
+## NPM Package
+
+```
+yarn add molstar
+```
+
+or
+
+```
+npm install molstar
+```
+
+Mol* code can then be imported from the ``molstar/lib/...`` namespace, e.g.
+
+```ts
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+```
+
+## Clone from GitHub
+
+
+```
+git clone https://github.com/molstar/molstar.git
+cd molstar
+npm install
+npm run build
+```
+
+--------------------
+
+For a watch task to automatically rebuild the source code on changes, run
+
+```
+npm run dev
+```
+
+or if working just with the Viewer app for better performance
+
+```
+npm run dev:viewer
+```

docs/docs/misc/exporting-components.md

@@ -0,0 +1,59 @@
+# Exporting components
+
+Export components data can be useful to reproduce the same view in a different visualization software.
+To do that, one would need to loop over all components, extract its selection (for example by using atom indices) and its representations (type, coloring and sizing).
+
+### Getting assets / molecular files
+
+```js
+for (const { asset, file } of plugin.managers.asset.assets) {
+  const isFile = asset.asset.kind === 'url'
+  console.log(asset.asset.id)
+  console.log(isFile)
+  const data = await file.arrayBuffer()
+}
+```
+
+### Getting components per structure
+
+```js
+import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin-state/objects';
+//...
+
+const componentManager = plugin.managers.structure.component;
+for (const structure of componentManager.currentStructures) {
+  if (!structure.properties) {
+      continue;
+  }
+  const cell = plugin.state.data.select(structure.properties.cell.transform.ref)[0];
+  if (!cell || !cell.obj) {
+    continue;
+  }
+  const structureData = (cell.obj as PSO.Molecule.Structure).data;
+  for (const component of structure.components) {
+    if (!component.cell.obj) {
+      continue;
+    }
+    // For each component in each structure, display the content of the selection
+    Structure.eachAtomicHierarchyElement(component.cell.obj.data, {
+      atom: location => console.log(location.element)
+    });
+    for (const rep of component.representations) {
+      // For each representation of the component, display its type
+      console.log(rep.cell?.transform?.params?.type?.name)
+
+      // Also display the color for each atom
+      const colorThemeName = rep.cell.transform.params?.colorTheme.name;
+      const colorThemeParams = rep.cell.transform.params?.colorTheme.params;
+      const theme = plugin.representation.structure.themes.colorThemeRegistry.create(
+        colorThemeName || '',
+        { structure: structureData },
+        colorThemeParams
+      ) as ColorTheme<typeof colorThemeParams>;
+      Structure.eachAtomicHierarchyElement(component.cell.obj.data, {
+        atom: loc => console.log(theme.color(loc, false))
+      });
+    }
+  }
+}
+```

docs/docs/misc/interesting-pdb-entries.md

@@ -1,3 +1,5 @@
+# Interesting PDB Entries
+
 * Cyclic polymers (1sfi, 6dny, 1HVZ)
 * B-DNA (1bna)
 * Missing carbonyl oxygen (1gfl)
@@ -13,18 +15,20 @@
     * DZ has C1 instead of N1 (e.g. 6I4N)
     * DP has N5 instead of C5 and C7 instead of N7 (e.g. 6I4N)
 * Beta & Gamma peptides (e.g. 1GAC, 6PQF)
+* Helices of D-amino acids (e.g. 7QDI)
 * Mixed (heterogeneous) all-atom/trace-only RNA model (1JGQ)
 * Polymers with residues with missing trace atoms (e.g. 2QFJ)
 * Modified RNA bases (1y26, 5L4O)
 * Discontinuous chains, i.e. gaps in the sequence (3sn6)
 * Lots of sheets (1cbs)
 * DNA (2np2, 1d66)
-* C-alpha only (2rcj)
+* C-alpha only (2RCJ, 6ZIG, 5AJ2)
 * Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible (6SW3)
 * Close backbone atoms but not linked (e.g. 4HIV)
 * Non-standard residues
     * Protein (1BRR, 5Z6Y)
     * DNA (5D3G)
+    * Collagen (6JEC)
 * Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
 * Long linear sugar chain (4HG6)
 * Anisotropic B-factors/Ellipsoids (1EJG)
@@ -34,7 +38,17 @@
     * ACE (many, e.g. 5AGU, 1E1X)
     * ACY in 7ABY
     * NH2 (many, e.g. 6Y13)
-
-Assembly symmetries
-* 5M30 (Assembly 1, C3 local and pseudo)
-* 1RB8 (Assembly 1, I global)
+* Ligands with many rings
+    * STU (e.g. 1U59) - many fused rings
+    * HT (e.g. 127D) - rings connected by a single bond
+    * J2C (e.g. 7EFJ) - rings connected by a single atom
+    * RBF (e.g. 7QF2) - three linearly fused rings
+    * TA1 (e.g. 1JFF) - many fused rings (incl. a 8-member rings)
+    * BPA (e.g. 1JDG) - many fused rings
+    * CLR (e.g. 3GKI) - four fused rings
+* Assembly symmetries
+    * 5M30 (Assembly 1, C3 local and pseudo)
+    * 1RB8 (Assembly 1, I global)
+* Deuterium atoms
+    * 3CWH (XUL with D and DOD)
+    * 8TT8 (HOH and other with D)

docs/docs/plugin/custom-library.md

@@ -0,0 +1,193 @@
+# Building a Custom Library
+
+This page goes over creating a custom Mol\* based library usable inside a `<script>` tag in an HTML page using the `esbuild` tool.
+
+## Setup
+
+- Create a new npm/yarn package
+- Install `molstar` and `esbuild` packages
+
+```
+mkdir molstar-lib
+cd molstar-lib
+npm init
+npm install molstar
+npm install esbuild --save-dev
+```
+
+## Example Library Code
+
+Create new file `src/index.ts` (or `.js` if you don't want to use TypeScript):
+
+```ts
+import { DefaultPluginSpec, PluginSpec } from 'molstar/lib/mol-plugin/spec';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+
+export async function initViewer(element: string | HTMLDivElement, options?: { spec?: PluginSpec }) {
+    const parent = typeof element === 'string' ? document.getElementById(element)! as HTMLDivElement : element;
+    const canvas = document.createElement('canvas') as HTMLCanvasElement;
+    parent.appendChild(canvas);
+
+    const spec = options?.spec ?? DefaultPluginSpec();
+
+    const plugin = new PluginContext(spec);
+    await plugin.init();
+
+    plugin.initViewer(canvas, parent);
+
+    return plugin;
+}
+
+export async function loadStructure(
+    plugin: PluginContext,
+    url: string,
+    options?: { format?: string, isBinary?: boolean }
+) {
+    const data = await plugin.builders.data.download(
+        { url, isBinary: options?.isBinary }
+    );
+    const trajectory = await plugin.builders.structure.parseTrajectory(
+        data,
+        options?.format ?? 'mmcif' as any
+    );
+    const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+    return preset;
+}
+```
+
+## Building the Library
+
+Add new commands to the `scripts` section of the `package.json` file
+
+```json
+"scripts": {
+  "build": "esbuild src/index.ts --bundle --outfile=./build/js/index.js --global-name=molstarLib",
+  "watch": "esbuild src/index.ts --bundle --outfile=./build/js/index.js --global-name=molstarLib --watch"
+}
+```
+
+and run the command `npm run build` (or `watch` for interactive development experience). This will create `build/js/index.js` file which can be imported with a `<script>` tag and the exported functions called view the `molstarLib` prefix (you can customize this parameter).
+
+## Using the Library
+
+Create file `build/index.html`:
+
+```html
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* Library Example</title>
+    </head>
+    <style>
+        #viewer {
+            position: absolute;
+            width: 800px;
+            height: 600px;
+        }
+    </style>
+    <script type="text/javascript" src="./js/index.js"></script>
+    <body>
+        <div id="viewer"></div>
+        <script type="text/javascript">
+            async function init() {1
+                const plugin = await molstarLib.initViewer("viewer");
+                await molstarLib.loadStructure(
+                    plugin,
+                    "https://models.rcsb.org/4hhb.bcif",
+                    { isBinary: true }
+                );
+            }
+            init();
+        </script>
+    </body>
+</html>
+```
+
+After opening `index.html` in a browser, you should see 
+
+![lib-example](lib-example.png)
+
+## Using Mol* React UI
+
+The above example does not make use of the default Mol\* React UI and any UI components are therefore the author's responsibility. The below examples show how to (re)use the Mol\* React UI.
+
+- Create `src/ui.tsx`:
+```tsx
+import React from 'react';
+import { createRoot } from 'react-dom/client';
+
+import { DefaultPluginUISpec, PluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
+import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
+import { Plugin } from 'molstar/lib/mol-plugin-ui/plugin';
+
+export async function initViewerUI(element: string | HTMLDivElement, options?: { spec?: PluginUISpec }) {
+    const parent = typeof element === 'string' ? document.getElementById(element)! as HTMLDivElement : element;
+    const spec = { ...DefaultPluginUISpec(), ...options?.spec };
+    const plugin = new PluginUIContext(spec);
+    await plugin.init();
+
+    createRoot(parent).render(<Plugin plugin={plugin} />)
+
+    return plugin;
+}
+
+export async function loadStructure(plugin: PluginUIContext, url: string, options?: { format?: string, isBinary?: boolean }) {
+    const data = await plugin.builders.data.download({ url, isBinary: options?.isBinary });
+    const trajectory = await plugin.builders.structure.parseTrajectory(data, options?.format ?? 'mmcif' as any);
+    await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+}
+```
+- Create `src/style.scss`:
+```scss
+@use '../node_modules/molstar/lib/mol-plugin-ui/skin/light.scss';
+```
+- Create `build/ui.html`:
+```html
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* UI Library Example</title>
+    </head>
+    <link rel="stylesheet" type="text/css" href="css/style.css" />
+    <style>
+        #viewer {
+            position: absolute;
+            inset: 0;
+        }
+    </style>
+    <script type="text/javascript" src="./js/ui.js"></script>
+    <body>
+        <div id="viewer"></div>
+        <script type="text/javascript">
+            async function init() {
+                const plugin = await molstarLib.initViewerUI("viewer", {
+                    spec: {
+                        layout: {
+                            initial: {
+                                isExpanded: true,
+                                showControls: true,
+                            },
+                        },
+                    }
+                });
+                await molstarLib.loadStructure(plugin, "https://models.rcsb.org/4hhb.bcif", { isBinary: true });
+            }
+            init();
+        </script>
+    </body>
+</html>
+```
+
+- Install `sass`: `npm install sass -save-dev` (or use [`esbuild` plugin](https://www.npmjs.com/package/esbuild-sass-plugin) and `import` the scss file in `ui.tsx`)
+- Add scripts to `package.json`:
+```json
+"build-ui": "esbuild src/ui.tsx --bundle --outfile=./build/js/ui.js --global-name=molstarLib",
+"css": "sass src/style.scss ./build/css/style.css"
+```
+- Run `npm run build-ui` and `npm run css` (skip if using `esbuild-sass-plugin`)
+- Opening `build/ui.html`:
+![ui-example](ui-example.png)

docs/docs/plugin/data-state.md

@@ -23,7 +23,7 @@ interface Snapshot {
 
 When defining the state object, all components are optional, i.e., it is possible to define just the ``data`` component.
 
-Example state is available [here](example-state.json). In the plugin, it is possible to create and load these objects using ``Download JSON`` 
+Example state is available [here](./example-state.json). In the plugin, it is possible to create and load these objects using ``Download JSON`` 
 and ``Open JSON`` buttons in the ``State Snapshots`` section.
 
 # State Tree
@@ -69,7 +69,7 @@ interface Transform.Props {
 }
 ```
 
-"Built-in" data state transforms and description of their parameters are defined in ``mol-plugin/state/transforms``. Behavior transforms are defined in ``mol-plugin/behavior``. Auto-generated documentation for the transforms is also [available](transforms.md).
+"Built-in" data state transforms and description of their parameters are defined in ``mol-plugin/state/transforms``. Behavior transforms are defined in ``mol-plugin/behavior``.
 
 # Animation State
 

docs/docs/plugin/examples.md

@@ -0,0 +1,3 @@
+# Plugin Examples
+
+Refer to Mol* [Apps](https://github.com/molstar/molstar/tree/master/src/apps) and [Examples](https://github.com/molstar/molstar/tree/master/src/examples).

docs/docs/plugin/file-formats.md

@@ -0,0 +1,44 @@
+
+Support file formats and their extensions.
+
+## Structure
+
+- MMCIF and CIFCORE (mmCIF and coreCIF schemas): cif, bcif, mmcif, mcif
+- GRO: gro
+- MOL: mol
+- MOL2: mol2
+- PDB/PDBQT: pdb, ent, pdbqt
+- SDF: sdf, sd
+- XYZ: xyz
+
+
+## Topology
+
+Need to be loaded together with Coordinates.
+
+- PRMTOP: prmtop, parm7
+- PSF: psf
+- TOP: top
+
+## Coordinates
+
+Need to be loaded together with a Structure or Topology.
+
+- DCD: dcd
+- NCTRAJ: nc, nctraj
+- TRR: trr
+- XTC: xtc
+
+
+## Volume
+
+- CCP4/MRC/MAP: ccp4, mrc, map
+- CUBE (may include a Structure): cub, cube
+- DSN6/BRIX: dsn6, brix
+- DX and DXBIN: dx, dxbin
+- DSCIF (DensityServer CIF schema): cif, bcif
+
+
+## Shape
+
+- PLY

docs/docs/plugin/instance.md

@@ -0,0 +1,301 @@
+# Creating Plugin Instance
+
+
+## Intro
+
+What is a plugin? A plugin is a collection of modules that provide functionality to the `Mol*` UI. The plugin is responsible for managing the state of the viewer, internal and user interactions. It has been a previous point of confusion for new users of `Mol*` to associate the __viewer__ part of the library with what is further referred to as the __plugin__. These two are closely connected in the `molstar-plugin-ui` module, which is the user-facing part of the library and ultimately provides the viewer, but they are ultimately distinct. 
+
+
+It is recommended that you inspect the general class structure of [`PluginInitWrapper`](https://github.com/molstar/molstar/blob/6edbae80db340134341631f669eec86543a0f1a8/src/mol-plugin-ui/plugin.tsx#L41), [`PluginUIContext`](https://github.com/molstar/molstar/blob/6edbae80db340134341631f669eec86543a0f1a8/src/mol-plugin-ui/context.ts#L12) and [`PluginUIComponent`](https://github.com/molstar/molstar/blob/6edbae80db340134341631f669eec86543a0f1a8/src/mol-plugin-ui/base.tsx#L16) to better understand the flow of data and events in the plugin. 
+A passing analogy is that a [ `PluginContext` ](https://github.com/molstar/molstar/blob/6edbae80db340134341631f669eec86543a0f1a8/src/mol-plugin/context.ts#L71) is the engine that powers computation, rendering, events and subscriptions inside the molstar UI. All UI components depend on `PluginContext`. 
+
+
+
+There are 4 basic ways of instantiating the Mol* plugin.
+
+## ``Viewer`` wrapper
+
+- The most basic usage is to use the ``Viewer`` wrapper. This is best suited for use cases that do not require custom behavior and are mostly about just displaying a structure.
+- See ``Viewer`` class is defined in [src/apps/viewer/app.ts](https://github.com/molstar/molstar/blob/master/src/apps/viewer/app.ts) for available methods
+- See [options.ts](https://github.com/molstar/molstar/blob/master/src/apps/viewer/options.ts) for available plugin options
+- See [embedded.html](https://github.com/molstar/molstar/blob/master/src/apps/viewer/embedded.html) and [mvs.html](https://github.com/molstar/molstar/blob/master/src/apps/viewer/mvs.html) for example usage
+- Importing `molstar.js` will expose `molstar.lib` namespace that allow accessing various functionality without a bundler such as WebPack or esbuild. See the `mvs` example above for basic usage.
+- Alternative color themes can be used by importing `theme/dark.css` (or `light/blue`) instead of `molstar.css`
+
+### molstar.js and molstar.css sources
+
+- Download `molstar` NPM package and use the files from `build/viewer` diractory
+- Use `jsdelivr` CDN
+  - `<script type="text/javascript" src="https://cdn.jsdelivr.net/npm/molstar@latest/build/viewer/molstar.js" />`
+  - `<link rel="stylesheet" type="text/css" href="https://cdn.jsdelivr.net/npm/molstar@latest/build/viewer/molstar.css" />`
+  - `@latest` can be replaced by a specific Mol* version, e.g., `@5.4.2`
+- Clone & build the GitHub repository
+  - This option allows for quite straightforward extension customization, e.g., not including movie export, which reduces the bundle size by ~0.5MB
+
+### Bundle size
+
+By default, the `Viewer` includes all the available extensions. This increases the bundle size significantly, especially by including the `mp4-export`, which is responsible for almost `0.5MB` of compressed bundle size. 
+It is quite easy to reduce this bundle size by cloning the Mol\* repository, editing [extensions.ts](https://github.com/molstar/molstar/blob/master/src/apps/viewer/options.ts) and rebuilding it with `npm run build:apps`. The new build will be available 
+in the `build/viewer` directory (the JS file you will find there is uncompressed, but your hosting setup should include automatic gzip compression, significantly reducing the size).
+
+Alternatively, you can explore building your own "viewer" using the base Mol\* library. For this, see the options below.
+
+
+### Example
+
+```HTML
+<style>
+    #app {
+        position: absolute;
+        left: 100px;
+        top: 100px;
+        width: 800px;
+        height: 600px;
+    }
+</style>
+<!-- 
+    molstar.js and .css are obtained from
+    - the folder build/viewer after cloning and building the molstar package 
+    - from the build/viewer folder in the Mol* NPM package
+-->
+<link rel="stylesheet" type="text/css" href="./molstar.css" />
+<script type="text/javascript" src="./molstar.js"></script>
+
+<div id="app"></div>
+
+<script type="text/javascript">
+    molstar.Viewer.create('app', {
+        layoutIsExpanded: false,
+        layoutShowControls: false,
+        layoutShowRemoteState: false,
+        layoutShowSequence: true,
+        layoutShowLog: false,
+        layoutShowLeftPanel: true,
+
+        viewportShowExpand: true,
+        viewportShowSelectionMode: false,
+        viewportShowAnimation: false,
+
+        pdbProvider: 'rcsb',
+        emdbProvider: 'rcsb',
+    }).then(viewer => {
+        viewer.loadPdb('7bv2');
+        viewer.loadEmdb('EMD-30210', { detail: 6 });
+    });
+</script>
+```
+
+### Using WebPack/esbuild/...
+
+When using WebPack (or other bundler) with the Mol* NPM package installed, the viewer class can be imported using 
+
+```ts
+import { Viewer } from 'molstar/lib/apps/viewer/app'
+
+function initViewer(target: string | HTMLElement) {
+    return Viewer.create(target, { /* options */}) // returns a Promise
+}
+```
+
+## ``PluginContext`` with built-in React UI
+
+- For more customization options it is possible to use the [``PluginContext``](https://github.com/molstar/molstar/blob/master/src/mol-plugin/context.ts) directly.
+- When creating the plugin instance it is possible to customize the [``PluginSpec``](https://github.com/molstar/molstar/blob/master/src/mol-plugin/spec.ts).
+- The default [``PluginSpec``](https://github.com/molstar/molstar/blob/master/src/mol-plugin/spec.ts) is available [here](https://github.com/molstar/molstar/blob/master/src/mol-plugin/spec.ts).
+- [``PluginConfig``](https://github.com/molstar/molstar/blob/master/src/mol-plugin/config.ts) object provides additional customization options.
+- See the [Viewer State Management](viewer-state.md) section for more information on customizing things like background.
+- See the [Data State Management](data-state.md) section for more information on build the state.
+
+```ts
+import { DefaultPluginUISpec, PluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
+import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
+import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
+import { PluginConfig } from 'molstar/lib/mol-plugin/config';
+
+const MySpec: PluginUISpec = {
+    ...DefaultPluginUISpec(),
+    config: [
+        [PluginConfig.VolumeStreaming.Enabled, false]
+    ]
+}
+
+async function createPlugin(parent: HTMLElement) {
+    const plugin = await createPluginUI({
+      target: parent,
+      spec: MySpec,
+      render: renderReact18
+    });
+
+    const data = await plugin.builders.data.download({ url: '...' }, { state: { isGhost: true } });
+    const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+    await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+
+    return plugin;
+}
+
+createPlugin(document.getElementById('app')!); // app is a <div> element with position: relative
+```
+
+To use the plugin (with the React UI) inside another React app:
+
+A single-plugin setup is shown the example below. In order to initialize multiple
+plugins, each with its own context and viewport, some extra steps are required (docs section to be added).
+
+```ts
+import { useEffect, createRef } from "react";
+import { createPluginUI } from "molstar/lib/mol-plugin-ui";
+import { renderReact18 } from "molstar/lib/mol-plugin-ui/react18";
+import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context";
+/*  Might require extra configuration,
+see https://webpack.js.org/loaders/sass-loader/ for example.
+create-react-app should support this natively. */
+import "molstar/lib/mol-plugin-ui/skin/light.scss";
+
+declare global {
+  interface Window {
+    molstar?: PluginUIContext;
+  }
+}
+
+
+export function MolStarWrapper() {
+  const parent = createRef<HTMLDivElement>();
+
+  // In debug mode of react's strict mode, this code will
+  // be called twice in a row, which might result in unexpected behavior.
+  useEffect(() => {
+    // By default, react will call each useEffect twice if using Strict mode in
+    // debug build, it is recommended to disable strict mode for this reason if possible
+    async function init() {
+        window.molstar = await createPluginUI({
+          target: parent.current as HTMLDivElement,
+          render: renderReact18
+        });
+
+        const data = await window.molstar.builders.data.download(
+          { url: "https://files.rcsb.org/download/3PTB.pdb" }, /* replace with your URL */
+          { state: { isGhost: true } }
+        );
+        const trajectory =
+          await window.molstar.builders.structure.parseTrajectory(data, "pdb");
+        await window.molstar.builders.structure.hierarchy.applyPreset(
+          trajectory,
+          "default"
+        );
+    }
+    init();
+    return () => {
+      window.molstar?.dispose();
+      window.molstar = undefined;
+    };
+  }, []);
+
+  return <div ref={parent} style={{ width: 640, height: 480 }}/>;
+}
+
+```
+
+
+Furthermore, if it is desirable in your project to use the `molstar`'s React UI components, but you wish to alter or rearrange the layout, you should take a look at the signatures of [ `PluginUIComponent` ](https://github.com/molstar/molstar/blob/6edbae80db340134341631f669eec86543a0f1a8/src/mol-plugin-ui/base.tsx#L16) which every "control" subclasses. 
+
+
+[ `SequenceView` ](https://github.com/molstar/molstar/blob/6edbae80db340134341631f669eec86543a0f1a8/src/mol-plugin-ui/sequence.tsx#L221C4-L221C4), for example, can be used separately from the `PluginUI`. Yet you would need to pass the `PluginUIContext` to it in order for it to observe the changes in the state of the plugin. This can be done via a `PluginContextContainer`:
+```typescript
+// your_app.plugin: PluginUIContext
+...
+<div className="your_custom_ui">
+  <PluginContextContainer plugin={your_app.plugin}>
+    <SequenceView />
+  </PluginContextContainer>
+</div>
+```
+
+## Directly using Mol* React UI
+
+```ts
+class MolStarWrapper {
+  private resolveInit: () => void;
+  initialized = new Promise<boolean>(res => { this.resolveInit = () => res(true); });
+
+  private initCalled = false;
+  plugin: PluginUIContext;
+  async init() {
+    if (this.initCalled) return;
+    this.initCalled = true;
+    this.plugin = ...;
+    await this.plugin.init();
+    this.resolveInit();
+  }
+}
+
+function MolStar({ model }: { model: MolStarWrapper }) {
+  const [initialized, setInitialized] = useState(false);
+  useEffect(() => {
+     async function init() {
+       await model.init();
+       setInitialized(true);
+     }
+     init();
+  }, [model]);
+
+  if (!initialized) return <>Loading</>;
+  return <div style={{ ..., position: 'relative' }}>
+    <Plugin plugin={model.plugin} />
+  </div>;
+}
+```
+
+## ``PluginContext`` without built-in React UI
+
+- The [``PluginContext``](https://github.com/molstar/molstar/blob/master/src/mol-plugin/context.ts) can be instantiated without using the default React UI.
+
+```HTML
+<div id='molstar-parent' style='position: absolute; top: 0; left: 0; right: 0; bottom: 0'>
+    <canvas id='molstar-canvas' style='position: absolute; top: 0; left: 0; right: 0; bottom: 0'></canvas>
+</div>
+```
+
+```ts
+import { DefaultPluginSpec, PluginSpec } from 'molstar/lib/mol-plugin/spec';
+import { PluginContext  } from 'molstar/lib/mol-plugin/context';
+import { PluginConfig } from 'molstar/lib/mol-plugin/config';
+
+const MySpec: PluginSpec = {
+    ...DefaultPluginSpec(),
+    config: [
+        [PluginConfig.VolumeStreaming.Enabled, false]
+    ]
+}
+
+async function init() {
+    const plugin = new PluginContext(MySpec);
+    await plugin.init();
+
+    const canvas = <HTMLCanvasElement> document.getElementById('molstar-canvas');
+    const parent = <HTMLDivElement> document.getElementById('molstar-parent');
+
+    if (!(await plugin.initViewerAsync(canvas, parent))) {
+        console.error('Failed to init Mol*');
+        return;
+    }
+
+    // Example url:"https://files.rcsb.org/download/3j7z.pdb" 
+    // Example url:"https://files.rcsb.org/download/5AFI.cif" 
+    const data = await plugin.builders.data.download({ url: '...' }, { state: { isGhost: true } });
+    const trajectory = await plugin.builders.structure.parseTrajectory(data, format); //format is 'mmcif' or 'pdb' etc.
+    await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+}
+
+```
+
+## ``Canvas3D`` without built-in state management
+
+- The ``PluginContext`` object from the above examples can be completely omitted.
+- See [Browser Tests](https://github.com/molstar/molstar/tree/master/src/tests/browser) for example usage.
+
+```ts
+const canvas = document.getElementById('canvas'); // parent <canvas> element
+const canvas3d = Canvas3D.create(Canvas3DContext.fromCanvas(canvas));
+canvas3d.animate();
+// use the canvas3d object here
+```

docs/docs/plugin/managers/markdown-extensions.md

@@ -0,0 +1,107 @@
+# Markdown Extension Manager
+
+The `markdownExtensions` manager in `PluginContext.manager` allows customizing
+the `Markdown` React component to enable executing commands and rendering custom content.
+
+The main use case of this is enriching [MolViewSpec](`https://molstar.org/mol-view-spec`) support.
+
+## API
+
+- `PluginContext.manager.markdownExtensions.register*` functions can be used to register extensions and state/data resolvers to make the the manager work with plugin extension
+- `PluginContext.manager.markdownExtensions.remove*` can be used to dynamically remove the above
+
+## Commands
+
+Extends Markdown Hyperlink syntax to support expressions of the form `[title](!c1=v1&c2=v2&...)` into an executable command. The command can be executed either on click, mouse enter, or mouse leave.
+
+Generally, the command should be URL encoded, e.g., `a b` => `a%20b` (in JS, `encodeURIComponent`, in Python `urllib.parse.quote_plus/urlencode`).
+
+### Built-in Commands
+
+- `center-camera` - Centers the camera
+- `apply-snapshot=key` - Loads snapshots with the provided key
+- `next-snapshot[=-1|1]` - Loads next/previous snapshot, the direction is optional and default to `1`
+- `play-snapshots` - Starts playback of state snapshots
+- `play-transition` - Plays an animation associated with the given snapshot
+- `stop-animation` - Stops currently playing animation
+- `focus-refs=ref1,ref2,...` - On click, focuses nodes with the provided refs
+- `highlight-refs=ref1,ref2,...` - On mouse over, highlights the provided refs
+- `query=...&lang=...&action=highlight,focus&focus-radius=...`
+    - `query` is an expression (e.g., `resn HEM` when using PyMol syntax)
+    - (optional) `lang` is one of `mol-script` (default), `pymol`, `vmd`, `jmol`
+    - (optional) `action` is an array of `highlight` (default), `focus` (multiple actions can be specified)
+    - (optional) `focus-radius` is extra distance applied when focusing the selection (default is `3`)
+    - Example: `[HEM](!query=resn%20HEM%26lang=pymol&action=highlight,focus)` highlights or focuses the HEM residue (the query must be URL encoded because it contains spaces and possibly other special characters)
+- `play-audio=src`, `toggle-audio[=src]`, `stop-audio`, `pause-audio`, `dispose-audio` - Audio playback support
+
+## Custom Content
+
+Extends Markdown Image syntax to support expressions of the form `![alt](!c1=v1&c2=v2&...)` to render custom elements instead.
+
+### Built-in Custom Content
+- `color-swatch=color` - Renders a box with the provided color
+-  Color palettes:
+    - `color-palette-name=name` - Renders a gradient with the provided named color palette (see `mol-util/color/lists.ts` for supported color schemes)
+    - `color-palette-colors=color1,color2` - Renders a gradient with the provided colors
+    - `color-palette-width=CCS-value` - Specifies the width of the element, defaults to `150px`
+    - `color-palette-height=CCS-value` - Specified the height of the element, defaults to `0.5em`
+    - `color-palette-discrete` - Renders discrete color list instead of interpolating
+
+
+## Example
+
+```markdown
+### Highlight/Focus:
+- ![blue](!color-swatch=blue) [polymer](!highlight-refs=polymer&focus-refs=polymer)
+- ![blue](!color-swatch=red) [ligand](!highlight-refs=ligand&focus-refs=ligand)
+- [both](!highlight-refs=polymer,ligand&focus-refs=polymer,ligand)
+
+### Color Palettes
+|name|visual|
+|---:|---|
+|viridis|![viridis](!color-palette-name=viridis)|
+|rainbow (discrete)|![simple-rainbow](!color-palette-name=simple-rainbow&color-palette-discrete)|
+|custom|![custom](!color-palette-colors=red,#00ff00,rgb(0,0,255))|
+
+### Camera controls
+- [center](!center-camera)
+
+### Image embedded in MVSX file
+![mvsx image](logo.png)
+```
+
+This works with the MolViewSpec state built by:
+
+```py
+import molviewspec as mvs
+
+builder = mvs.create_builder()
+
+assets = {
+    "1cbs.cif": "https://files.wwpdb.org/download/1cbs.cif",
+    "logo.png": "https://molstar.org/img/molstar-logo.png",
+}
+
+model = (
+    builder.download(url="1cbs.cif")
+        .parse(format="mmcif")
+        .model_structure()
+)
+(
+    model.component(selector="polymer")
+    .representation(ref="polymer")
+    .color(color="blue")
+)
+(
+    model.component(selector="ligand")
+    .representation(ref="ligand")
+    .color(color="red")
+)
+
+mvsx = mvs.MVSX(
+    data=builder.get_state(
+        description="""..."""  # inline the code above
+    ),
+    assets=assets
+)
+```

docs/docs/plugin/selections.md

@@ -0,0 +1,190 @@
+# Selections
+
+
+## Basic Concepts
+
+### Location
+
+The selection model in Mol\* is based on a generic concept called *location*. A location is a pointer to a selectable element within a scene. For example:
+
+- A structure element location (an atom or a coarse element) is an object composed of `{ structure: Structure, unit: Unit, element: UnitIndex }` (you can think of a `Unit` as a generalized chain)
+- A bond location is very similar to structure element, requiring pointers to two units and elements
+- A "shape" (generally a mesh) location consists of pointer to the parent shape and a group of triangles
+
+### Loci
+
+Structures and other renderable elements generally consist of many locations and simply using a list of locations would be 
+prohibitively expensive (e.g., large selections in structures with hundreds of thousands of atoms).
+
+This is why Mol\* introduces
+the concept of `Loci` &mdash; a compressed representation of multiple locations. Instead of having a list of structure element locations (`{ structure: Structure, unit: Unit, element: UnitIndex }[]`), the representation becomes (simplified) `{ structure: Structure, unit: Unit, elements: OrderedSet<UnitIndex> }`. The ordered set can be further compressed for continuous ranges, keeping only the index of the 1st and last element.
+
+### Bundle
+
+Locations and loci point to the raw JavaScript data structures representing the underlying molecules, making them not serializable in JSON. A *bundle* is a serializable version of the loci.
+
+### Structure Queries
+
+Defining selections directly using the loci would be very cumbersome. For this reason, Mol\* includes the [MolQl query language](https://molql.org) to help define selections.
+
+
+## Selection Methods
+
+Assuming you have a model already loaded into the plugin (see [Creating Plugin Instance](./instance.md)), these are some of the methods you can use to create selections.
+
+### MolQL (`mol-script`) language
+
+[MolQL](https://molql.org) (`mol-script`) is a language for addressing crystallographic structures and is a part of the Mol* library found at `https://github.com/molstar/molstar/tree/master/src/mol-script`. It can be used against the Molstar plugin as a query language and transpiled against multiple external molecular visualization libraries(see [here](https://github.com/molstar/molstar/tree/master/src/mol-script/transpilers)).
+
+**Example:** Querying a structure for a specific chain and residue range
+
+Select residues with `12<res_id<200 of chain with auth_asym_id=A`
+
+```typescript
+import { compileIdListSelection } from 'molstar/lib/mol-script/util/id-list'
+
+const query = compileIdListSelection('A 12-200', 'auth');
+window.molstar?.managers.structure.selection.fromCompiledQuery('add',query);
+```
+
+### Selection Queries
+
+Another way to create a selection is via a `SelectionQuery` object. This is a more programmatic way to create a selection. The following example shows how to select a chain and a residue range using a `SelectionQuery` object.
+This relies on the concept of `Expression` which is basically a intermediate representation between a Molscript statement and a selection query. 
+ 
+**Example:** Select residues 10-15 of chains A and F in a structure using a `SelectionQuery` object
+
+```typescript
+import { MolScriptBuilder as MS, MolScriptBuilder } from 'molstar/lib/mol-script/language/builder';
+import { Expression } from 'molstar/lib/mol-script/language/expression';
+import {  StructureSelectionQuery } from 'molstar/lib/mol-plugin-state/helpers/structure-selection-query'
+
+
+export function select_multiple() {
+
+ const args = [['A', 10, 15], ['F', 10, 15]]
+ const groups: Expression[] = [];
+ for (var chain of args) {
+   groups.push(MS.struct.generator.atomGroups({
+     'chain-test': MS.core.rel.eq([MolScriptBuilder.struct.atomProperty.macromolecular.auth_asym_id(), chain[0]]),
+     'residue-test': MS.core.rel.inRange([MolScriptBuilder.struct.atomProperty.macromolecular.label_seq_id(), chain[1], chain[2]])
+   }));
+ }
+ var sq = StructureSelectionQuery('residue_range_10_15_in_A_and_F', MS.struct.combinator.merge(groups))
+ mstar.managers.structure.selection.fromSelectionQuery('set', sq)
+}
+```
+
+Complex queries can be constructed by combining primitive queries at the level of [`chain-test`, `residue-test`, `entity-test`, etc] (https://github.com/molstar/molstar/blob/6edbae80db340134341631f669eec86543a0f1a8/src/mol-script/language/symbol-table/structure-query.ts#L88C4-L94C112) by combining them via logical connectives provided in the `MolscriptBuilder.core.rel` as above.
+
+Inspect these examples to get a better feeling for this syntax: `https://github.com/molstar/molstar/blob/6edbae80db340134341631f669eec86543a0f1a8/src/mol-plugin-state/helpers/structure-selection-query.ts#L88-L580`
+
+
+Furthermore, a query made this way can be converted to a `Loci` object which is important in many parts of the libary:
+```typescript
+// Select residue 124 of chain A and convert to Loci
+const Q = MolScriptBuilder;
+var sel = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
+  'chain-test': Q.core.rel.eq([Q.struct.atomProperty.macromolecular.auth_asym_id(), A]),
+  'residue-test': Q.core.rel.eq([Q.struct.atomProperty.macromolecular.label_seq_id(), 124]),
+}), objdata)
+
+let loci = StructureSelection.toLociWithSourceUnits(sel);
+```
+
+### Query Functions
+
+Instead of building expressions, query functions can be created directly, e.g.:
+
+```ts
+import { atoms } from 'mol-model/structure/query/queries/generators';
+
+const query = atoms({
+  residueTest: ctx => {
+    const seqId = StructureProperties.residue.label_seq_id(ctx.element);
+    return seqId > 10 && seqId < 25;
+  },
+});
+
+const selection = query(new QueryContext(structure));
+// ...
+```
+
+### Selection Schema
+
+For simple selections, the `StructureElement.Schema` can be used to reference elements within a protein structure using mmCIF `atom_site` field names, e.g.:
+
+```ts
+const ala121: StructureElement.Schema = { label_asym_id: 'A', label_seq_id: 121 };
+const residues: StructureElement.Schema = { 
+  items: {
+    auth_asym_id: ['A', 'B'],
+    auth_seq_id: [10, 11],
+  }
+};
+
+const loci = StructureElement.Loci.fromSchema(structure, residues);
+```
+
+Usually, a code editor such as VS Code will auto-suggest all the available field names.
+
+### Using the `hierarchy` manager
+
+It is possible to select a subcomponent's data directly from the plugin manager.
+
+```typescript 
+import { Structure } from '../mol-model/structure';
+
+const ligandData = plugin.managers.structure.hierarchy.selection.structures[0]?.components[0]?.cell.obj?.data;
+const ligandLoci = Structure.toStructureElementLoci(ligandData as any);
+
+plugin.managers.camera.focusLoci(ligandLoci);
+plugin.managers.interactivity.lociSelects.select({ loci: ligandLoci });
+```
+
+## Selection Events
+If you want to subscribe to selection events (e.g. to change external state in your application based on a user selection), you can use: `plugin.behaviors.interaction.click.subscribe`
+
+Here's an example of passing in a React "set" function to update selected residue positions.
+```typescript
+import {
+  Structure,
+  StructureProperties,
+} from "molstar/lib/mol-model/structure"
+// setSelected is assumed to be a "set" function returned by useState
+// (selected: any[]) => void
+plugin.behaviors.interaction.click.subscribe(
+  (event: InteractivityManager.ClickEvent) => {
+    const selections = Array.from(
+      plugin.managers.structure.selection.entries.values()
+    );
+    // This bit can be customized to record any piece information you want
+    const localSelected: any[] = [];
+    for (const { structure } of selections) {
+      if (!structure) continue;
+      Structure.eachAtomicHierarchyElement(structure, {
+        residue: (loc) => {
+          const position = StructureProperties.residue.label_seq_id(loc);
+          localSelected.push({ position });
+        },
+      });
+    }
+    setSelected(localSelected);
+  }
+)
+```
+
+## Helper Functions
+
+Given an `Expression`, `QueryFn`, or `StructureElement.Schema` it is possible to use `fromExpression/Query/Schema` functions on `StructureElement.Loci` and `StructureElement.Bundle`.
+
+### `Viewer` app
+
+The `Viewer` app provides the `structureInteractivity` function which allows easy selection/highlighting of the loaded structure. For example:
+
+```ts
+viewer.structureInteractivity({
+    elements: { beg_auth_seq_id: 10, end_auth_seq_id: 50 },
+    action: 'select',
+});
+```

docs/docs/plugin/superposition.md

@@ -0,0 +1,152 @@
+# Structure Superposition
+
+Mol* provides utilities for superposing protein structures, including both sequence-independent (RMSD-based) and structure-based (TM-align) methods.
+
+## RMSD-based Superposition
+
+The basic superposition method uses the Kabsch algorithm to minimize RMSD between corresponding atoms:
+
+```typescript
+import { superpose } from 'molstar/lib/mol-model/structure/structure/util/superposition';
+import { StructureSelection, QueryContext } from 'molstar/lib/mol-model/structure';
+import { compile } from 'molstar/lib/mol-script/runtime/query/compiler';
+import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
+
+// Create a query for C-alpha atoms
+const caQuery = compile<StructureSelection>(MS.struct.generator.atomGroups({
+    'atom-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_atom_id(), 'CA'])
+}));
+
+// Get selections from two structures
+const sel1 = StructureSelection.toLociWithCurrentUnits(caQuery(new QueryContext(structure1)));
+const sel2 = StructureSelection.toLociWithCurrentUnits(caQuery(new QueryContext(structure2)));
+
+// Compute superposition (returns transformation matrices)
+const transforms = superpose([sel1, sel2]);
+
+// transforms[0].bTransform contains the Mat4 to superpose structure2 onto structure1
+```
+
+## TM-align Superposition
+
+TM-align is a structure-based alignment algorithm that produces the TM-score, a length-independent metric for comparing protein structures. Unlike RMSD, TM-score is normalized to [0, 1] and is more robust for comparing proteins of different sizes.
+
+### Basic Usage
+
+```typescript
+import { tmAlign } from 'molstar/lib/mol-model/structure/structure/util/tm-align';
+import { StructureElement } from 'molstar/lib/mol-model/structure';
+
+// Get C-alpha Loci from two structures (see selection examples above)
+const loci1: StructureElement.Loci = /* ... */;
+const loci2: StructureElement.Loci = /* ... */;
+
+// Run TM-align
+const result = tmAlign(loci1, loci2);
+
+console.log('TM-score (normalized by structure 1):', result.tmScoreA);
+console.log('TM-score (normalized by structure 2):', result.tmScoreB);
+console.log('RMSD:', result.rmsd);
+console.log('Aligned residues:', result.alignedLength);
+
+// result.bTransform is a Mat4 to transform structure2 onto structure1
+```
+
+### TM-align Result
+
+The `tmAlign` function returns a `TMAlignResult` object with the following properties:
+
+| Property | Type | Description |
+|----------|------|-------------|
+| `bTransform` | `Mat4` | Transformation matrix to superpose structure B onto A |
+| `tmScoreA` | `number` | TM-score normalized by length of structure A |
+| `tmScoreB` | `number` | TM-score normalized by length of structure B |
+| `rmsd` | `number` | RMSD of aligned residue pairs (in Angstroms) |
+| `alignedLength` | `number` | Number of aligned residue pairs |
+| `sequenceIdentity` | `number` | Sequence identity of aligned residues (0-1) |
+| `alignmentA` | `number[]` | Indices of aligned residues in structure A |
+| `alignmentB` | `number[]` | Indices of aligned residues in structure B |
+
+### Understanding TM-score
+
+The TM-score is calculated as:
+
+$$\text{TM-score} = \frac{1}{L} \sum_{i=1}^{L_{ali}} \frac{1}{1 + (d_i/d_0)^2}$$
+
+Where:
+- $L$ is the length of the reference protein
+- $L_{ali}$ is the number of aligned residues
+- $d_i$ is the distance between the $i$-th pair of aligned residues after superposition
+- $d_0 = 1.24 \sqrt[3]{L - 15} - 1.8$ is a length-dependent normalization factor
+
+**TM-score interpretation:**
+- TM-score > 0.5: Generally indicates proteins with the same fold
+- TM-score > 0.17: Generally indicates proteins with random structural similarity
+
+### Low-level API
+
+For direct coordinate-based alignment without structures, use the `TMAlign` namespace:
+
+```typescript
+import { TMAlign } from 'molstar/lib/mol-math/linear-algebra/3d/tm-align';
+
+// Create position arrays
+const posA = TMAlign.Positions.empty(lengthA);
+const posB = TMAlign.Positions.empty(lengthB);
+
+// Fill in coordinates
+for (let i = 0; i < lengthA; i++) {
+    posA.x[i] = /* x coordinate */;
+    posA.y[i] = /* y coordinate */;
+    posA.z[i] = /* z coordinate */;
+}
+// ... similarly for posB
+
+// Compute alignment
+const result = TMAlign.compute({ a: posA, b: posB });
+```
+
+### Complete Example: Aligning Two PDB Structures
+
+```typescript
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
+import { compile } from 'molstar/lib/mol-script/runtime/query/compiler';
+import { StructureSelection, QueryContext, StructureElement } from 'molstar/lib/mol-model/structure';
+import { tmAlign } from 'molstar/lib/mol-model/structure/structure/util/tm-align';
+import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
+import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
+
+async function alignStructures(plugin: PluginContext, structure1: any, structure2: any) {
+    // Query for C-alpha atoms in chain A
+    const caQuery = compile<StructureSelection>(MS.struct.generator.atomGroups({
+        'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.auth_asym_id(), 'A']),
+        'atom-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_atom_id(), 'CA'])
+    }));
+
+    // Get structure data
+    const data1 = structure1.cell?.obj?.data;
+    const data2 = structure2.cell?.obj?.data;
+
+    // Create selections
+    const sel1 = StructureSelection.toLociWithCurrentUnits(caQuery(new QueryContext(data1)));
+    const sel2 = StructureSelection.toLociWithCurrentUnits(caQuery(new QueryContext(data2)));
+
+    // Run TM-align
+    const result = tmAlign(sel1, sel2);
+
+    // Apply transformation to structure2
+    const b = plugin.state.data.build().to(structure2)
+        .insert(StateTransforms.Model.TransformStructureConformation, {
+            transform: { name: 'matrix', params: { data: result.bTransform, transpose: false } }
+        });
+    await plugin.runTask(plugin.state.data.updateTree(b));
+
+    return result;
+}
+```
+
+## References
+
+- Zhang Y, Skolnick J. "TM-align: a protein structure alignment algorithm based on the TM-score." *Nucleic Acids Research* 33, 2302-2309 (2005). DOI: [10.1093/nar/gki524](https://doi.org/10.1093/nar/gki524)
+- Kabsch W. "A solution for the best rotation to relate two sets of vectors." *Acta Crystallographica* A32, 922-923 (1976).

docs/docs/plugin/transforms/custom-conformation.md

@@ -0,0 +1,45 @@
+# Assign custom conformation to a Model
+
+This document shows how to update model conformation dynamically using the `ModelWithCoordinates` transforms. If this does not work well with your particular use case, it is suggested to write a custom version of `ModelWithCoordinates` with similar usage as outlined in this document.
+
+```ts
+async function animateFirstXCoordinateExample(plugin: PluginContext, url: string, format: BuiltInTrajectoryFormat) {
+    // Load data
+    const _data = await plugin.builders.data.download({ url });
+    const trajectory = await plugin.builders.structure.parseTrajectory(_data, format);
+    const hierarchy = await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+    if (!hierarchy) return;
+
+    // Insert ModelWithCoordinates cell to be updated in the loop bellow
+    const coordinatesNode = await plugin.build().to(hierarchy!.model).insert(ModelWithCoordinates).commit();
+
+    const x0 = hierarchy!.model.data!.atomicConformation.x[0];
+    let xOffset = 0;
+    async function animateFirstXCoord() {
+        // Normally, the whole conformation would come from an API/library call, but here we fake it:
+        const { x, y, z } = hierarchy!.model.data!.atomicConformation;
+        const nextX = [...(x as number[])];
+        nextX[0] = x0 + xOffset;
+        xOffset += 0.05;
+        if (xOffset > 1) xOffset = 0;
+
+        // Construct new coodinate frame from the data and commit the update.
+        // Rest of the state tree will reconcile automatically.
+        await plugin.build().to(coordinatesNode).update({
+            atomicCoordinateFrame: {
+                elementCount: x.length,
+                time: { value: 0, unit: 'step' },
+                xyzOrdering: { isIdentity: true },
+                x: nextX,
+                y,
+                z,
+            }
+        }).commit();
+
+        requestAnimationFrame(animateFirstXCoord);
+    }
+    animateFirstXCoord();
+}
+
+// animateFirstXCoordinateExample('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2244/record/SDF/?record_type=3d', 'sdf');
+```

docs/docs/plugin/transforms/custom-trajectory.md

@@ -0,0 +1,72 @@
+# Load Trajectory from a Custom Format
+
+This section shows a high level example for loading trajectory from custom data in specialized plugin instances. A more complete solution is available for example in form of the [G3D format extension](https://github.com/molstar/molstar/tree/master/src/extensions/g3d).
+
+## Defining and Using a Custom Transformer
+
+```ts
+import { StateTransformer } from 'molstar/lib/mol-state';
+
+const CreateTransformer = StateTransformer.builderFactory('custom-namespace');
+
+export interface CustomTrajectoryData {
+    // ...
+}
+
+export const TrajectoryFromCustomData = CreateTransformer({
+    name: 'trajectory-from-custom-data',
+    display: 'Trajectory',
+    from: PluginStateObject.Root,
+    to: PluginStateObject.Molecule.Trajectory,
+    params: {
+        data: PD.Value<CustomTrajectoryData>(void 0 as any, { isHidden: true }),
+    },
+})({
+    apply({ params }) {
+        return Task.create('Trajectory', async (ctx) => {
+            const models = await customParse(params.data, ctx);
+            return new PluginStateObject.Molecule.Trajectory(models, {
+                label: 'Trajectory',
+            });
+        });
+    },
+});
+```
+
+The ``customParse`` function can usually be implemented 
+by modifying/extending an [existing parser already available in Mol*](https://github.com/molstar/molstar/tree/master/src/mol-model-formats/structure).
+
+To use the transformer:
+
+```ts
+const data: CustomTrajectoryData = await (await fetch(url)).json();
+const trajectory = await plugin.build().toRoot().apply(TrajectoryFromCustomData, { data }).commit();
+// Create the representation
+await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+```
+
+## Using Mol* to Download the Data
+
+```ts
+export const TrajectoryFromCustomData = CreateTransformer({
+    name: 'trajectory-from-custom-data',
+    display: 'Trajectory',
+    from: PluginStateObject.Data.String, // or PluginStateObject.Data.Binary
+    to: PluginStateObject.Molecule.Trajectory,
+})({
+    apply({ a }) {
+        return Task.create('Trajectory', async (ctx) => {
+            const models = await customParse(a.data, ctx);
+            return new PluginStateObject.Molecule.Trajectory(models, {
+                label: 'Trajectory',
+            });
+        });
+    },
+});
+
+//////////////
+
+const data = await plugin.builders.data.download({ url, isBinary });
+const trajectory = await plugin.build().to(data).apply(TrajectoryFromCustomData, { data }).commit();
+await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+```

docs/docs/plugin/viewer-state.md

@@ -0,0 +1,132 @@
+# Viewer State Management
+
+## ``Canvas3D`` Properties
+Properties of the [``Canvas3D``](https://github.com/molstar/molstar/blob/master/src/mol-canvas3d/canvas3d.ts) can be 
+changed using [``PluginCommands``](https://github.com/molstar/molstar/blob/master/src/mol-plugin/commands.ts).  
+
+
+### Change background, highlight, or select color
+```ts
+import { ColorNames } from 'molstar/lib/mol-util/color/names';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+
+const renderer = plugin.canvas3d!.props.renderer;
+PluginCommands.Canvas3D.SetSettings(plugin, { settings: { renderer: { ...renderer, backgroundColor: ColorNames.red /* or: 0xff0000 as Color */ } } });
+```
+Similarly, `highlightColor` and `selectColor` can be updated.
+
+
+## Interactivity
+
+Interactivity in Mol* is based on the concept of ``Loci``. A ``Loci`` usually references a collection of objects and can be created by a [``Selection``](selections.md). For example, the
+``Loci`` captures all atoms in the chain with label_asym_id B of a protein:
+```ts
+import { Script } from 'molstar/lib/mol-script/script';
+import { StructureSelection } from 'molstar/lib/mol-model/structure/query';
+
+const data = plugin.managers.structure.hierarchy.current.structures[0]?.cell.obj?.data;
+if (!data) return;
+
+const selection = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
+    'chain-test': Q.core.rel.eq(['B', Q.ammp('label_asym_id')])
+}), data);
+const loci = StructureSelection.toLociWithSourceUnits(selection);
+```
+A ``Loci`` can be used to trigger custom [``Behaviors``](#behaviors).
+
+
+### Log message to Mol* console
+The built-in console in the bottom center of the plugin shows log entries.
+```ts
+plugin.log.message('This message will appear in the Mol* console');
+```
+Other log levels are: `info`, `warn`, and `error`.
+
+
+### Show toast message
+Toast messages will appear in the bottom right of the plugin and will linger for a limited time before disappearing.
+```ts
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
+
+PluginCommands.Toast.Show(plugin, {
+    title: 'Custom Message',
+    message: 'A custom toast message that will disappear after 2 seconds.',
+    key: 'toast-custom',
+    timeoutMs: 2000
+});
+```
+
+## Behaviors
+
+The state of the Mol* plugin is usually governed by dynamic behaviors which can be set up in initial plugin specification or updated during the plugin runtime. This allows for high modularity and customizability of individual plugin instances.
+
+
+### Highlight ``Loci``
+Highlighting adds a transient overpaint to a representation that will linger until the mouse enters hovers over another 
+object. Highlights can be applied to a previously defined ``Loci`` by:
+```ts
+plugin.managers.interactivity.lociHighlights.highlightOnly({ loci }); // loci: Loci
+```
+Reset all highlights by:
+```ts
+plugin.managers.interactivity.clearHighlights();
+```
+
+
+### Select ``Loci``
+
+Selected elements will appear with distinct visuals and, if applicable, the corresponding sequence positions will be 
+shown in the Sequence Viewer panel. Selections persist until removed, for example by clicking the background. A ``Loci``
+is selected by:
+```ts
+plugin.managers.interactivity.lociSelects.select({ loci }); // loci: Loci
+```
+
+Deselect a specific ``Loci`` by:
+```ts
+plugin.managers.interactivity.lociSelects.deselect({ loci }); // loci: Loci
+```
+To deselect everything:
+```ts
+plugin.managers.interactivity.lociSelects.deselectAll();
+```
+
+
+### Focus ``Loci``
+The focus representation shows a ``Loci`` in ball-and-stick representation and, additionally, visualizes non-covalent
+interactions between atoms of the ``Loci`` as well as interactions with surrounding residues (default: 5 Å).
+```ts
+plugin.managers.structure.focus.setFromLoci(loci);
+```
+Extend an existing focus representation by:
+```ts
+plugin.managers.structure.focus.addFromLoci(loci); // loci: Loci
+```
+Reset by:
+```ts
+plugin.managers.structure.focus.clear();
+```
+
+
+### Zoom ``Loci``
+A ``Loci`` can also be used to manipulate the camera. Zoom in by:
+```ts
+plugin.managers.camera.focusLoci(loci); // loci: Loci
+```
+
+Restore the default camera position by:
+```ts
+plugin.managers.camera.reset();
+```
+
+### Turn off view resetting on new representations
+A new representation via something like
+```ts
+.apply(StateTransforms.Representation.VolumeRepresentation3D, ...)
+```
+can reset the view to make the whole representation visible.
+When one wants to keep the view the same instead of having the rep reset the view,
+keep the view constant by:
+```ts
+plugin.canvas3d?.setProps({ camera: { manualReset: true } });
+```

docs/mkdocs.yml

@@ -0,0 +1,65 @@
+site_name: Mol* Developer Documentation
+theme:
+  name: material
+
+  # 404 page
+  static_templates:
+    - 404.html
+
+  # Necessary for search to work properly
+  include_search_page: false
+  search_index_only: true
+
+  # Default values, taken from mkdocs_theme.yml
+  language: en
+  font:
+    text: Roboto
+    code: Roboto Mono
+  favicon: assets/favicon.png
+  icon:
+    logo: logo
+markdown_extensions:
+  - pymdownx.highlight
+  - pymdownx.superfences
+  - pymdownx.arithmatex:
+      generic: true
+# Scripts for rendering Latex equations (in addition to pymdownx.arithmatex):
+extra_javascript:
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
+nav:
+  - 'index.md'
+  - Plugin:
+    - Creating Instance: 'plugin/instance.md'
+    - Examples: plugin/examples.md
+    - Custom Library: 'plugin/custom-library.md'
+    - Selections: 'plugin/selections.md'
+    - Superposition: 'plugin/superposition.md'
+    - Viewer State: 'plugin/viewer-state.md'
+    - Data State: 'plugin/data-state.md'
+    - File Formats: 'plugin/file-formats.md'
+    - CIF Schemas: 'plugin/cif-schemas.md'
+    - Managers:
+      - Markdown Extensions: 'plugin/managers/markdown-extensions.md'
+    - State Transforms:
+      - Custom Trajectory: 'plugin/transforms/custom-trajectory.md'
+      - Custom Conformation: 'plugin/transforms/custom-conformation.md'
+  - Data Access Tools:
+    - 'data-access-tools/model-server.md'
+    - Volume Server:
+      - Overview: 'data-access-tools/volume-server/index.md'
+      - Examples: 'data-access-tools/volume-server/examples.md'
+      - How it Works: 'data-access-tools/volume-server/how-it-works.md'
+      - Data Format: 'data-access-tools/volume-server/response-data-format.md'
+    - 'data-access-tools/plugin-state-server.md'
+    - 'data-access-tools/convert-to-bcif.md'
+    - 'data-access-tools/create-ccd-table.md'
+    - 'data-access-tools/extract-ccd-ions.md'
+  - Extensions:
+    - MolViewSpec: 'extensions/mvs/index.md'
+    - wwPDB StructConn: 'extensions/struct-conn.md'
+    - Tunnels: 'extensions/tunnels.md'
+    - Interactions: 'extensions/interactions.md'
+  - Misc:
+    - Interesting PDB entries: misc/interesting-pdb-entries.md
+    - Exporting component data: misc/exporting-components.md
+repo_url: https://github.com/molstar/docs

docs/model-server/readme.md

@@ -1,69 +0,0 @@
-Model Server
-============
-
-Model Server is a tool for preprocessing and querying macromolecular structure data.
-
-Installing and Running
-=====================
-
-Requires nodejs 8+.
-
-## From GitHub
-
-```
-git clone https://github.com/molstar/molstar
-npm install
-```
-
-Afterwards, build the project source:
-
-```
-npm run build-tsc
-```
-
-and run the server by 
-
-```
-node lib/commonjs/servers/model/server/server
-```
-
-## From NPM
-
-```
-npm install --production molstar
-./model-server 
-```
-
-(or ``node node_modules\.bin\model-server`` in Windows).
-
-The NPM package contains all the tools mentioned here as "binaries":
-
-- ``model-server``
-- ``model-server-query``
-- ``model-server-preprocess``
-
-
-### Production use
-
-In production it is required to use a service that will keep the server running, such as [forever.js](https://github.com/foreverjs/forever).
-
-
-### Memory issues
-
-Sometimes nodejs might run into problems with memory. This is usually resolved by adding the ``--max-old-space-size=8192`` parameter.
-
-## Preprocessor
-
-The preprocessor application allows to add custom data to CIF files and/or convert CIF to BinaryCIF. ``node lib/commonjs/servers/model/preprocess`` or ``model-server-preprocess`` binary from the NPM package.
-
-
-## Local Mode
-
-The server can be run in local/file based mode using ``node lib/commonjs/servers/model/query`` (``model-server-query`` binary from the NPM package).
-
-Custom Properties
-=================
-
-This feature is still in development.
-
-It is possible to provide property descriptors that transform data to internal representation and define how it should be exported into one or mode CIF categories. Examples of this are located in the ``mol-model-props`` module and are linked to the server in the config and ``servers/model/properties``.

docs/state/transforms.md

@@ -1,738 +0,0 @@
-# Mol* Plugin State Transformer Reference
-
-* [build-in.root](#build-in-root)
-* [ms-plugin.download](#ms-plugin-download)
-* [ms-plugin.read-file](#ms-plugin-read-file)
-* [ms-plugin.parse-cif](#ms-plugin-parse-cif)
-* [ms-plugin.parse-ccp4](#ms-plugin-parse-ccp4)
-* [ms-plugin.parse-dsn6](#ms-plugin-parse-dsn6)
-* [ms-plugin.trajectory-from-mmcif](#ms-plugin-trajectory-from-mmcif)
-* [ms-plugin.trajectory-from-pdb](#ms-plugin-trajectory-from-pdb)
-* [ms-plugin.model-from-trajectory](#ms-plugin-model-from-trajectory)
-* [ms-plugin.structure-from-model](#ms-plugin-structure-from-model)
-* [ms-plugin.structure-assembly-from-model](#ms-plugin-structure-assembly-from-model)
-* [ms-plugin.structure-symmetry-from-model](#ms-plugin-structure-symmetry-from-model)
-* [ms-plugin.structure-selection](#ms-plugin-structure-selection)
-* [ms-plugin.structure-complex-element](#ms-plugin-structure-complex-element)
-* [ms-plugin.custom-model-properties](#ms-plugin-custom-model-properties)
-* [ms-plugin.volume-from-ccp4](#ms-plugin-volume-from-ccp4)
-* [ms-plugin.volume-from-dsn6](#ms-plugin-volume-from-dsn6)
-* [ms-plugin.representation-highlight-loci](#ms-plugin-representation-highlight-loci)
-* [ms-plugin.representation-select-loci](#ms-plugin-representation-select-loci)
-* [ms-plugin.default-loci-label-provider](#ms-plugin-default-loci-label-provider)
-* [ms-plugin.structure-representation-3d](#ms-plugin-structure-representation-3d)
-* [ms-plugin.explode-structure-representation-3d](#ms-plugin-explode-structure-representation-3d)
-* [ms-plugin.volume-representation-3d](#ms-plugin-volume-representation-3d)
-* [ms-plugin.focus-loci-on-select](#ms-plugin-focus-loci-on-select)
-* [ms-plugin.pdbe-structure-quality-report-prop](#ms-plugin-pdbe-structure-quality-report-prop)
-* [ms-plugin.rcsb-assembly-symmetry-prop](#ms-plugin-rcsb-assembly-symmetry-prop)
-* [ms-plugin.structure-animation](#ms-plugin-structure-animation)
-* [ms-plugin.scene-labels](#ms-plugin-scene-labels)
-
-----------------------------
-## <a name="build-in-root"></a>build-in.root :: () -> ()
-*For internal use.*
-
-----------------------------
-## <a name="ms-plugin-download"></a>ms-plugin.download :: Root -> String | Binary
-*Download string or binary data from the specified URL*
-
-### Parameters
-- **url**: String *(Resource URL. Must be the same domain or support CORS.)*
-- **label**?: String
-- **isBinary**?: true/false *(If true, download data as binary (string otherwise))*
-
-### Default Parameters
-```js
-{
-  "url": "https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif"
-}
-```
-----------------------------
-## <a name="ms-plugin-read-file"></a>ms-plugin.read-file :: Root -> String | Binary
-*Read string or binary data from the specified file*
-
-### Parameters
-- **file**: JavaScript File Handle
-- **label**?: String
-- **isBinary**?: true/false *(If true, open file as as binary (string otherwise))*
-
-### Default Parameters
-```js
-{}
-```
-----------------------------
-## <a name="ms-plugin-parse-cif"></a>ms-plugin.parse-cif :: String | Binary -> Cif
-*Parse CIF from String or Binary data*
-
-----------------------------
-## <a name="ms-plugin-parse-ccp4"></a>ms-plugin.parse-ccp4 :: Binary -> Ccp4
-*Parse CCP4/MRC/MAP from Binary data*
-
-----------------------------
-## <a name="ms-plugin-parse-dsn6"></a>ms-plugin.parse-dsn6 :: Binary -> Dsn6
-*Parse CCP4/BRIX from Binary data*
-
-----------------------------
-## <a name="ms-plugin-trajectory-from-mmcif"></a>ms-plugin.trajectory-from-mmcif :: Cif -> Trajectory
-*Identify and create all separate models in the specified CIF data block*
-
-### Parameters
-- **blockHeader**?: String *(Header of the block to parse. If none is specifed, the 1st data block in the file is used.)*
-
-### Default Parameters
-```js
-{}
-```
-----------------------------
-## <a name="ms-plugin-trajectory-from-pdb"></a>ms-plugin.trajectory-from-pdb :: String -> Trajectory
-
-----------------------------
-## <a name="ms-plugin-model-from-trajectory"></a>ms-plugin.model-from-trajectory :: Trajectory -> Model
-*Create a molecular structure from the specified model.*
-
-### Parameters
-- **modelIndex**: Numeric value *(Zero-based index of the model)*
-
-### Default Parameters
-```js
-{
-  "modelIndex": 0
-}
-```
-----------------------------
-## <a name="ms-plugin-structure-from-model"></a>ms-plugin.structure-from-model :: Model -> Structure
-*Create a molecular structure from the specified model.*
-
-----------------------------
-## <a name="ms-plugin-structure-assembly-from-model"></a>ms-plugin.structure-assembly-from-model :: Model -> Structure
-*Create a molecular structure assembly.*
-
-### Parameters
-- **id**?: String *(Assembly Id. Value 'deposited' can be used to specify deposited asymmetric unit.)*
-
-### Default Parameters
-```js
-{}
-```
-----------------------------
-## <a name="ms-plugin-structure-symmetry-from-model"></a>ms-plugin.structure-symmetry-from-model :: Model -> Structure
-*Create a molecular structure symmetry.*
-
-### Parameters
-- **ijkMin**: 3D vector [x, y, z]
-- **ijkMax**: 3D vector [x, y, z]
-
-### Default Parameters
-```js
-{
-  "ijkMin": [
-    -1,
-    -1,
-    -1
-  ],
-  "ijkMax": [
-    1,
-    1,
-    1
-  ]
-}
-```
-----------------------------
-## <a name="ms-plugin-structure-selection"></a>ms-plugin.structure-selection :: Structure -> Structure
-*Create a molecular structure from the specified query expression.*
-
-### Parameters
-- **query**: Value
-- **label**?: String
-
-### Default Parameters
-```js
-{}
-```
-----------------------------
-## <a name="ms-plugin-structure-complex-element"></a>ms-plugin.structure-complex-element :: Structure -> Structure
-*Create a molecular structure from the specified model.*
-
-### Parameters
-- **type**: One of 'atomic-sequence', 'water', 'atomic-het', 'spheres'
-
-### Default Parameters
-```js
-{
-  "type": "atomic-sequence"
-}
-```
-----------------------------
-## <a name="ms-plugin-custom-model-properties"></a>ms-plugin.custom-model-properties :: Model -> Model
-
-### Parameters
-- **properties**: Array of  *(A list of property descriptor ids.)*
-
-### Default Parameters
-```js
-{
-  "properties": []
-}
-```
-----------------------------
-## <a name="ms-plugin-volume-from-ccp4"></a>ms-plugin.volume-from-ccp4 :: Ccp4 -> Data
-*Create Volume from CCP4/MRC/MAP data*
-
-### Parameters
-- **voxelSize**: 3D vector [x, y, z]
-
-### Default Parameters
-```js
-{
-  "voxelSize": [
-    1,
-    1,
-    1
-  ]
-}
-```
-----------------------------
-## <a name="ms-plugin-volume-from-dsn6"></a>ms-plugin.volume-from-dsn6 :: Dsn6 -> Data
-*Create Volume from DSN6/BRIX data*
-
-### Parameters
-- **voxelSize**: 3D vector [x, y, z]
-
-### Default Parameters
-```js
-{
-  "voxelSize": [
-    1,
-    1,
-    1
-  ]
-}
-```
-----------------------------
-## <a name="ms-plugin-representation-highlight-loci"></a>ms-plugin.representation-highlight-loci :: Root -> Behavior
-
-----------------------------
-## <a name="ms-plugin-representation-select-loci"></a>ms-plugin.representation-select-loci :: Root -> Behavior
-
-----------------------------
-## <a name="ms-plugin-default-loci-label-provider"></a>ms-plugin.default-loci-label-provider :: Root -> Behavior
-
-----------------------------
-## <a name="ms-plugin-structure-representation-3d"></a>ms-plugin.structure-representation-3d :: Structure -> Representation3D
-
-### Parameters
-- **type**: Object { name: string, params: object } where name+params are:
-  - **cartoon**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **doubleSided**: true/false
-      - **flipSided**: true/false
-      - **flatShaded**: true/false
-      - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
-      - **sizeFactor**: Numeric value
-      - **linearSegments**: Numeric value
-      - **radialSegments**: Numeric value
-      - **aspectRatio**: Numeric value
-      - **arrowFactor**: Numeric value
-      - **visuals**: Array of 'polymer-trace', 'polymer-gap', 'nucleotide-block', 'direction-wedge'
-
-  - **ball-and-stick**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **doubleSided**: true/false
-      - **flipSided**: true/false
-      - **flatShaded**: true/false
-      - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
-      - **sizeFactor**: Numeric value
-      - **detail**: Numeric value
-      - **linkScale**: Numeric value
-      - **linkSpacing**: Numeric value
-      - **radialSegments**: Numeric value
-      - **sizeAspectRatio**: Numeric value
-      - **visuals**: Array of 'element-sphere', 'intra-link', 'inter-link'
-
-  - **carbohydrate**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **doubleSided**: true/false
-      - **flipSided**: true/false
-      - **flatShaded**: true/false
-      - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
-      - **detail**: Numeric value
-      - **sizeFactor**: Numeric value
-      - **linkScale**: Numeric value
-      - **linkSpacing**: Numeric value
-      - **radialSegments**: Numeric value
-      - **linkSizeFactor**: Numeric value
-      - **visuals**: Array of 'carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'
-
-  - **distance-restraint**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **doubleSided**: true/false
-      - **flipSided**: true/false
-      - **flatShaded**: true/false
-      - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
-      - **linkScale**: Numeric value
-      - **linkSpacing**: Numeric value
-      - **radialSegments**: Numeric value
-      - **sizeFactor**: Numeric value
-
-  - **molecular-surface**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **doubleSided**: true/false
-      - **flipSided**: true/false
-      - **flatShaded**: true/false
-      - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
-      - **resolution**: Numeric value
-      - **radiusOffset**: Numeric value
-      - **smoothness**: Numeric value
-      - **useGpu**: true/false
-      - **ignoreCache**: true/false
-      - **sizeFactor**: Numeric value
-      - **lineSizeAttenuation**: true/false
-      - **visuals**: Array of 'gaussian-surface', 'gaussian-wireframe'
-
-  - **molecular-volume**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **isoValueNorm**: Numeric value *(Normalized Isolevel Value)*
-      - **renderMode**: One of 'isosurface', 'volume'
-      - **controlPoints**: A list of 2d vectors [xi, yi][]
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-      - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
-      - **resolution**: Numeric value
-      - **radiusOffset**: Numeric value
-      - **smoothness**: Numeric value
-
-  - **point**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **sizeFactor**: Numeric value
-      - **pointSizeAttenuation**: true/false
-      - **pointFilledCircle**: true/false
-      - **pointEdgeBleach**: Numeric value
-      - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
-
-  - **spacefill**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **doubleSided**: true/false
-      - **flipSided**: true/false
-      - **flatShaded**: true/false
-      - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
-      - **sizeFactor**: Numeric value
-      - **detail**: Numeric value
-
-
-- **colorTheme**: Object { name: string, params: object } where name+params are:
-  - **carbohydrate-symbol**:
-Object with:
-
-  - **chain-id**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **cross-link**:
-Object with:
-      - **domain**: Interval [min, max]
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **element-index**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **element-symbol**:
-Object with:
-
-  - **molecule-type**:
-Object with:
-
-  - **polymer-id**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **polymer-index**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **residue-name**:
-Object with:
-
-  - **secondary-structure**:
-Object with:
-
-  - **sequence-id**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **shape-group**:
-Object with:
-
-  - **unit-index**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **uniform**:
-Object with:
-      - **value**: Color as 0xrrggbb
-
-
-- **sizeTheme**: Object { name: string, params: object } where name+params are:
-  - **physical**:
-Object with:
-
-  - **shape-group**:
-Object with:
-
-  - **uniform**:
-Object with:
-      - **value**: Numeric value
-
-
-
-### Default Parameters
-```js
-{
-  "type": {
-    "name": "cartoon",
-    "params": {
-      "alpha": 1,
-      "useFog": true,
-      "highlightColor": 16737945,
-      "selectColor": 3407641,
-      "quality": "auto",
-      "doubleSided": false,
-      "flipSided": false,
-      "flatShaded": false,
-      "unitKinds": [
-        "atomic",
-        "spheres"
-      ],
-      "sizeFactor": 0.2,
-      "linearSegments": 8,
-      "radialSegments": 16,
-      "aspectRatio": 5,
-      "arrowFactor": 1.5,
-      "visuals": [
-        "polymer-trace"
-      ]
-    }
-  },
-  "colorTheme": {
-    "name": "polymer-id",
-    "params": {
-      "list": "RedYellowBlue"
-    }
-  },
-  "sizeTheme": {
-    "name": "uniform",
-    "params": {
-      "value": 1
-    }
-  }
-}
-```
-----------------------------
-## <a name="ms-plugin-explode-structure-representation-3d"></a>ms-plugin.explode-structure-representation-3d :: Representation3D -> Obj
-
-### Parameters
-- **t**: Numeric value
-
-### Default Parameters
-```js
-{
-  "t": 0
-}
-```
-----------------------------
-## <a name="ms-plugin-volume-representation-3d"></a>ms-plugin.volume-representation-3d :: Data -> Representation3D
-
-### Parameters
-- **type**: Object { name: string, params: object } where name+params are:
-  - **isosurface**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **doubleSided**: true/false
-      - **flipSided**: true/false
-      - **flatShaded**: true/false
-      - **isoValue**:       - **absolute**: Numeric value
-      - **relative**: Numeric value
-
-      - **sizeFactor**: Numeric value
-      - **lineSizeAttenuation**: true/false
-      - **visuals**: Array of 'solid', 'wireframe'
-
-  - **direct-volume**:
-Object with:
-      - **alpha**: Numeric value
-      - **useFog**: true/false
-      - **highlightColor**: Color as 0xrrggbb
-      - **selectColor**: Color as 0xrrggbb
-      - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **isoValueNorm**: Numeric value *(Normalized Isolevel Value)*
-      - **renderMode**: One of 'isosurface', 'volume'
-      - **controlPoints**: A list of 2d vectors [xi, yi][]
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-
-- **colorTheme**: Object { name: string, params: object } where name+params are:
-  - **carbohydrate-symbol**:
-Object with:
-
-  - **chain-id**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **cross-link**:
-Object with:
-      - **domain**: Interval [min, max]
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **element-index**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **element-symbol**:
-Object with:
-
-  - **molecule-type**:
-Object with:
-
-  - **polymer-id**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **polymer-index**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **residue-name**:
-Object with:
-
-  - **secondary-structure**:
-Object with:
-
-  - **sequence-id**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **shape-group**:
-Object with:
-
-  - **unit-index**:
-Object with:
-      - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
-
-  - **uniform**:
-Object with:
-      - **value**: Color as 0xrrggbb
-
-
-- **sizeTheme**: Object { name: string, params: object } where name+params are:
-  - **physical**:
-Object with:
-
-  - **shape-group**:
-Object with:
-
-  - **uniform**:
-Object with:
-      - **value**: Numeric value
-
-
-
-### Default Parameters
-```js
-{
-  "type": {
-    "name": "isosurface",
-    "params": {
-      "alpha": 1,
-      "useFog": true,
-      "highlightColor": 16737945,
-      "selectColor": 3407641,
-      "quality": "auto",
-      "doubleSided": false,
-      "flipSided": false,
-      "flatShaded": false,
-      "isoValue": {
-        "kind": "relative",
-        "stats": {
-          "min": 0,
-          "max": 0,
-          "mean": 0,
-          "sigma": 0
-        },
-        "relativeValue": 2
-      },
-      "sizeFactor": 1,
-      "lineSizeAttenuation": false,
-      "visuals": [
-        "solid"
-      ]
-    }
-  },
-  "colorTheme": {
-    "name": "uniform",
-    "params": {
-      "value": 13421772
-    }
-  },
-  "sizeTheme": {
-    "name": "uniform",
-    "params": {
-      "value": 1
-    }
-  }
-}
-```
-----------------------------
-## <a name="ms-plugin-focus-loci-on-select"></a>ms-plugin.focus-loci-on-select :: Root -> Behavior
-
-### Parameters
-- **minRadius**: Numeric value
-- **extraRadius**: Numeric value *(Value added to the boundning sphere radius of the Loci.)*
-
-### Default Parameters
-```js
-{
-  "minRadius": 10,
-  "extraRadius": 4
-}
-```
-----------------------------
-## <a name="ms-plugin-pdbe-structure-quality-report-prop"></a>ms-plugin.pdbe-structure-quality-report-prop :: Root -> Behavior
-
-### Parameters
-- **autoAttach**: true/false
-
-### Default Parameters
-```js
-{
-  "autoAttach": false
-}
-```
-----------------------------
-## <a name="ms-plugin-rcsb-assembly-symmetry-prop"></a>ms-plugin.rcsb-assembly-symmetry-prop :: Root -> Behavior
-
-### Parameters
-- **autoAttach**: true/false
-
-### Default Parameters
-```js
-{
-  "autoAttach": false
-}
-```
-----------------------------
-## <a name="ms-plugin-structure-animation"></a>ms-plugin.structure-animation :: Root -> Behavior
-
-### Parameters
-- **rotate**: true/false
-- **rotateValue**: Numeric value
-- **explode**: true/false
-- **explodeValue**: Numeric value
-
-### Default Parameters
-```js
-{
-  "rotate": false,
-  "rotateValue": 0,
-  "explode": false,
-  "explodeValue": 0
-}
-```
-----------------------------
-## <a name="ms-plugin-scene-labels"></a>ms-plugin.scene-labels :: Root -> Behavior
-
-### Parameters
-- **alpha**: Numeric value
-- **useFog**: true/false
-- **highlightColor**: Color as 0xrrggbb
-- **selectColor**: Color as 0xrrggbb
-- **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-- **fontFamily**: One of 'sans-serif', 'monospace', 'serif', 'cursive'
-- **fontQuality**: One of '0', '1', '2', '3', '4'
-- **fontStyle**: One of 'normal', 'italic', 'oblique'
-- **fontVariant**: One of 'normal', 'small-caps'
-- **fontWeight**: One of 'normal', 'bold'
-- **sizeFactor**: Numeric value
-- **borderWidth**: Numeric value
-- **borderColor**: Color as 0xrrggbb
-- **offsetX**: Numeric value
-- **offsetY**: Numeric value
-- **offsetZ**: Numeric value
-- **background**: true/false
-- **backgroundMargin**: Numeric value
-- **backgroundColor**: Color as 0xrrggbb
-- **backgroundOpacity**: Numeric value
-- **attachment**: One of 'bottom-left', 'bottom-center', 'bottom-right', 'middle-left', 'middle-center', 'middle-right', 'top-left', 'top-center', 'top-right'
-- **levels**: Array of 'structure', 'polymer', 'ligand'
-
-### Default Parameters
-```js
-{
-  "alpha": 1,
-  "useFog": true,
-  "highlightColor": 16737945,
-  "selectColor": 3407641,
-  "quality": "auto",
-  "fontFamily": "sans-serif",
-  "fontQuality": 3,
-  "fontStyle": "normal",
-  "fontVariant": "normal",
-  "fontWeight": "normal",
-  "sizeFactor": 1,
-  "borderWidth": 0,
-  "borderColor": 8421504,
-  "offsetX": 0,
-  "offsetY": 0,
-  "offsetZ": 0,
-  "background": true,
-  "backgroundMargin": 0.2,
-  "backgroundColor": 16775930,
-  "backgroundOpacity": 0.9,
-  "attachment": "middle-center",
-  "levels": []
-}
-```
-----------------------------

docs/volume-server/README.md

@@ -1,86 +0,0 @@
-What is VolumeServer
-=====================
-
-VolumeServer is a service for accessing subsets of volumetric density data. It automatically downsamples the data depending on the volume of the requested region to reduce the bandwidth requirements and provide near-instant access to even the largest data sets.
-
-It uses the text based CIF and BinaryCIF formats to deliver the data to the client. 
-
-For quick info about the benefits of using the server, check out the [examples](examples.md).
-
-Installing and Running
-=====================
-
-Requires nodejs 8+.
-
-## From GitHub
-
-```
-git clone https://github.com/molstar/molstar
-npm install
-```
-
-Afterwards, build the project source:
-
-```
-npm run build-tsc
-```
-
-and run the server by 
-
-```
-node lib/commonjs/servers/volume/server
-```
-
-## From NPM
-
-```
-npm install --production molstar
-./volume-server 
-```
-
-(or ``node node_modules\.bin\volume-server`` in Windows).
-
-The NPM package contains all the tools mentioned here as "binaries":
-
-- ``volume-server``
-- ``volume-server-pack``
-- ``volume-server-query``
-
-
-### Production use
-
-In production it is required to use a service that will keep the server running, such as [forever.js](https://github.com/foreverjs/forever).
-
-
-### Memory issues
-
-Sometimes nodejs might run into problems with memory. This is usually resolved by adding the ``--max-old-space-size=8192`` parameter.
-
-
-## Preparing the Data
-
-For the server to work, CCP4/MAP (models 0, 1, 2 are supported) input data need to be converted into a custom block format. 
-To achieve this, use the ``pack`` application (``node lib/commonjs/servers/volume/pack`` or ``volume-server-pack`` binary from the NPM package).
-
-## Local Mode
-
-The program  ``lib/commonjs/servers/volume/pack`` (``volume-server-query`` in NPM package) can be used to query the data without running a http server.
-
-## Navigating the Source Code
-
-The source code is split into 2 mains parts: ``pack`` and ``server``:
-
-- The ``pack`` part provides the means of converting CCP4 files into the internal block format.
-- The ``server`` includes
-  - ``query``: the main part of the server that handles a query. ``execute.ts`` is the "entry point".
-  - ``algebra``: linear, "coordinate", and "box" algebra provides the means for calculations necessary to concent a user query into a menaningful response.
-  - API wrapper that handles the requests.
-
-Consuming the Data 
-==================
-
-The data can be consumed in any (modern) browser using the [ciftools library](https://github.com/molstar/ciftools) (or any other piece of code that can read text or binary CIF).
-
-The [Data Format](DataFormat.md) document gives a detailed description of the server response format.
-
-As a reference/example of the server usage is available in Mol* ``mol-plugin`` module.

eslint.config.mjs

@@ -0,0 +1,111 @@
+import { defineConfig } from "eslint/config";
+import globals from "globals";
+import typescriptEslint from "@typescript-eslint/eslint-plugin";
+import tsParser from "@typescript-eslint/parser";
+
+export default defineConfig([{
+    ignores: [
+        "node_modules/*",
+        "build/*",
+        "deploy/*",
+        "docs/site/*",
+        "lib/*",
+        "eslint.config.mjs",
+        "build.mjs",
+    ]
+},{
+    languageOptions: {
+        globals: {
+            ...globals.browser,
+            ...globals.node,
+        },
+
+        ecmaVersion: 2018,
+        sourceType: "module",
+
+        parserOptions: {
+            ecmaFeatures: {
+                impliedStrict: true,
+            },
+        },
+    },
+
+    rules: {
+        indent: "off",
+        "arrow-parens": ["off", "as-needed"],
+        "brace-style": ["error", "1tbs", {
+            allowSingleLine: true,
+        }],
+        "comma-spacing": "off",
+        "space-infix-ops": "off",
+        "comma-dangle": "off",
+        quotes: ["warn", "single", { "allowTemplateLiterals": true, "avoidEscape": true }],
+        eqeqeq: ["error", "smart"],
+        "import/order": "off",
+        "no-eval": "warn",
+        "no-extend-native": "warn",
+        "no-new-wrappers": "warn",
+        "no-trailing-spaces": "error",
+        "no-unsafe-finally": "warn",
+        "no-self-compare": "warn",
+        "no-var": "error",
+        "spaced-comment": "error",
+        semi: "warn",
+        "no-restricted-syntax": ["error", {
+            selector: "ExportDefaultDeclaration",
+            message: "Default exports are not allowed",
+        }],
+        "no-throw-literal": "error",
+        "key-spacing": "error",
+        "object-curly-spacing": ["error", "always"],
+        "array-bracket-spacing": "error",
+        "space-in-parens": "error",
+        "computed-property-spacing": "error",
+        "prefer-const": ["error", {
+            destructuring: "all",
+            ignoreReadBeforeAssign: false,
+        }],
+        "space-before-function-paren": "off",
+        "func-call-spacing": "off",
+        "no-multi-spaces": "error",
+        "block-spacing": "error",
+        "keyword-spacing": "warn",
+        "space-before-blocks": "error",
+        "semi-spacing": "error",
+        "no-constant-binary-expression": "error",
+    },
+}, {
+    files: ["**/*.ts", "**/*.tsx"],
+
+    plugins: {
+        "@typescript-eslint": typescriptEslint,
+    },
+
+    languageOptions: {
+        parser: tsParser,
+        ecmaVersion: 5,
+        sourceType: "module",
+
+        parserOptions: {
+            project: ["tsconfig.eslint.json"],
+        },
+    },
+
+    rules: {
+        "@typescript-eslint/ban-types": "off",
+        "@typescript-eslint/class-name-casing": "off",        
+        "@typescript-eslint/member-delimiter-style": ["off", {
+            multiline: {
+                delimiter: "none",
+                requireLast: true,
+            },
+
+            singleline: {
+                delimiter: "semi",
+                requireLast: false,
+            },
+        }],
+        "@typescript-eslint/prefer-namespace-keyword": "warn",
+        "@typescript-eslint/semi": ["off", null],
+    },
+}]);

examples/docking/ligands_1.sdf

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+
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+  3  4  2  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  7  8  1  0
+  8  9  1  0
+  9 10  2  0
+ 10 11  1  0
+ 11 12  1  0
+ 12 13  1  0
+ 13 14  1  0
+ 14 15  1  0
+ 15 16  1  0
+ 16 17  1  0
+ 17 18  1  0
+ 18 19  1  0
+ 11 20  2  0
+ 20 21  1  0
+ 21 22  2  0
+ 22 23  1  0
+ 23 24  1  0
+ 24 25  2  0
+  7 26  2  0
+ 26  3  1  0
+ 25  9  1  0
+ 19 14  1  0
+ 24 20  1  0
+  1 27  1  0
+  1 28  1  0
+  1 29  1  0
+  4 30  1  0
+  5 31  1  0
+  6 32  1  0
+  8 33  1  0
+ 13 34  1  0
+ 13 35  1  0
+ 14 36  1  0
+ 15 37  1  0
+ 15 38  1  0
+ 16 39  1  0
+ 16 40  1  0
+ 17 41  1  0
+ 17 42  1  0
+ 18 43  1  0
+ 18 44  1  0
+ 19 45  1  0
+ 19 46  1  0
+ 22 47  1  0
+ 23 48  1  0
+ 26 49  1  0
+M  END
+>  <ligandCode>  (1) 
+forcefield_3904
+
+>  <ligandName>  (1) 
+klr_22
+
+$$$$
+forcefield_3905
+     RDKit          3D
+
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+$$$$

examples/mvs/1cbs-focus.mvsj

@@ -0,0 +1,115 @@
+{
+ "metadata": {
+  "title": "Example MolViewSpec - 1cbs with labelled and zoomed ligand",
+  "version": "1",
+  "timestamp": "2023-11-24T10:45:49.873Z"
+ },
+ "root": {
+  "kind": "root",
+  "children": [
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+    "kind": "download",
+    "params": {
+     "url": "https://www.ebi.ac.uk/pdbe/entry-files/1cbs.bcif"
+    },
+    "children": [
+     {
+      "kind": "parse",
+      "params": {
+       "format": "bcif"
+      },
+      "children": [
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+        "params": {
+         "type": "model"
+        },
+        "children": [
+         {
+          "kind": "component",
+          "params": {
+           "selector": "polymer"
+          },
+          "children": [
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+             "type": "cartoon"
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+               "color": "green"
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+               "selector": {
+                "label_asym_id": "A",
+                "end_label_seq_id": 50
+               },
+               "color": "#6688ff"
+              }
+             }
+            ]
+           },
+           {
+            "kind": "label",
+            "params": {
+             "text": "Protein"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": "ligand"
+          },
+          "children": [
+           {
+            "kind": "focus",
+            "params": {
+             "direction": [0.5, 0, -1],
+             "up": [0.365, 0.913, 0.183]
+            }
+           },
+           {
+            "kind": "representation",
+            "params": {
+             "type": "ball_and_stick"
+            },
+            "children": [
+             {
+              "kind": "color",
+              "params": {
+               "color": "#cc3399"
+              }
+             }
+            ]
+           },
+           {
+            "kind": "label",
+            "params": {
+             "text": "Retinoic Acid"
+            }
+           }
+          ]
+         }
+        ]
+       }
+      ]
+     }
+    ]
+   },
+   {
+    "kind": "canvas",
+    "params": {
+     "background_color": "#ffffee"
+    }
+   }
+  ]
+ }
+}

examples/mvs/1cbs.mvsj

@@ -0,0 +1,117 @@
+{
+ "metadata": {
+  "title": "Example MolViewSpec - 1cbs with labelled protein and ligand",
+  "version": "1",
+  "timestamp": "2023-11-24T10:38:17.483Z"
+ },
+ "root": {
+  "kind": "root",
+  "children": [
+   {
+    "kind": "download",
+    "params": {
+     "url": "https://www.ebi.ac.uk/pdbe/entry-files/1cbs.bcif"
+    },
+    "children": [
+     {
+      "kind": "parse",
+      "params": {
+       "format": "bcif"
+      },
+      "children": [
+       {
+        "kind": "structure",
+        "params": {
+         "type": "model"
+        },
+        "children": [
+         {
+          "kind": "component",
+          "params": {
+           "selector": "polymer"
+          },
+          "children": [
+           {
+            "kind": "representation",
+            "params": {
+             "type": "cartoon"
+            },
+            "children": [
+             {
+              "kind": "color",
+              "params": {
+               "color": "green"
+              }
+             },
+             {
+              "kind": "color",
+              "params": {
+               "selector": {
+                "label_asym_id": "A",
+                "beg_label_seq_id": 1,
+                "end_label_seq_id": 50
+               },
+               "color": "#6688ff"
+              }
+             }
+            ]
+           },
+           {
+            "kind": "label",
+            "params": {
+             "text": "Protein"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": "ligand"
+          },
+          "children": [
+           {
+            "kind": "representation",
+            "params": {
+             "type": "ball_and_stick"
+            },
+            "children": [
+             {
+              "kind": "color",
+              "params": {
+               "color": "#cc3399"
+              }
+             }
+            ]
+           },
+           {
+            "kind": "label",
+            "params": {
+             "text": "Retinoic Acid"
+            }
+           }
+          ]
+         }
+        ]
+       }
+      ]
+     }
+    ]
+   },
+   {
+    "kind": "canvas",
+    "params": {
+     "background_color": "#ffffee"
+    }
+   },
+   {
+    "kind": "camera",
+    "params": {
+     "target": [17, 21, 27],
+     "position": [41, 34, 69],
+     "up": [-0.129,0.966,-0.224]
+    }
+   }
+  ]
+ }
+}

examples/mvs/1h9t_domain_colors.mvsj

@@ -0,0 +1,67 @@
+{
+ "metadata": {
+  "title": "Example MolViewSpec - 1h9t colored by external annotation",
+  "version": "1",
+  "timestamp": "2023-11-24T10:47:33.182Z"
+ },
+ "root": {
+  "kind": "root",
+  "children": [
+   {
+    "kind": "download",
+    "params": {
+     "url": "https://www.ebi.ac.uk/pdbe/entry-files/1h9t.bcif"
+    },
+    "children": [
+     {
+      "kind": "parse",
+      "params": {
+       "format": "bcif"
+      },
+      "children": [
+       {
+        "kind": "structure",
+        "params": {
+         "type": "model"
+        },
+        "children": [
+         {
+          "kind": "component",
+          "params": {
+           "selector": "polymer"
+          },
+          "children": [
+           {
+            "kind": "representation",
+            "params": {
+             "type": "cartoon"
+            },
+            "children": [
+             {
+              "kind": "color",
+              "params": {
+               "selector": "all",
+               "color": "white"
+              }
+             },
+             {
+              "kind": "color_from_uri",
+              "params": {
+               "uri": "./1h9t_domains.json",
+               "format": "json",
+               "schema": "all_atomic"
+              }
+             }
+            ]
+           }
+          ]
+         }
+        ]
+       }
+      ]
+     }
+    ]
+   }
+  ]
+ }
+}

examples/mvs/1h9t_domain_labels.mvsj

@@ -0,0 +1,583 @@
+{
+ "metadata": {
+  "title": "Example MolViewSpec - 1h9t colored and labelled by external annotation",
+  "version": "1",
+  "timestamp": "2023-11-24T10:48:28.677Z"
+ },
+ "root": {
+  "kind": "root",
+  "children": [
+   {
+    "kind": "download",
+    "params": {
+     "url": "https://www.ebi.ac.uk/pdbe/entry-files/1h9t.bcif"
+    },
+    "children": [
+     {
+      "kind": "parse",
+      "params": {
+       "format": "bcif"
+      },
+      "children": [
+       {
+        "kind": "structure",
+        "params": {
+         "type": "model"
+        },
+        "children": [
+         {
+          "kind": "component",
+          "params": {
+           "selector": "protein"
+          },
+          "children": [
+           {
+            "kind": "representation",
+            "params": {
+             "type": "cartoon"
+            },
+            "children": [
+             {
+              "kind": "color",
+              "params": {
+               "selector": "all",
+               "color": "white"
+              }
+             },
+             {
+              "kind": "color_from_uri",
+              "params": {
+               "uri": "./1h9t_domains.json",
+               "format": "json",
+               "schema": "all_atomic"
+              }
+             }
+            ]
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": "nucleic"
+          },
+          "children": [
+           {
+            "kind": "representation",
+            "params": {
+             "type": "ball_and_stick"
+            },
+            "children": [
+             {
+              "kind": "color",
+              "params": {
+               "selector": "all",
+               "color": "white"
+              }
+             },
+             {
+              "kind": "color_from_uri",
+              "params": {
+               "uri": "./1h9t_domains.json",
+               "format": "json",
+               "schema": "all_atomic"
+              }
+             }
+            ]
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": "ion"
+          },
+          "children": [
+           {
+            "kind": "representation",
+            "params": {
+             "type": "surface"
+            },
+            "children": [
+             {
+              "kind": "color_from_uri",
+              "params": {
+               "uri": "./1h9t_domains.json",
+               "format": "json",
+               "schema": "all_atomic"
+              }
+             }
+            ]
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "beg_label_seq_id": 9,
+            "end_label_seq_id": 83
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "DNA-binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "B",
+            "beg_label_seq_id": 9,
+            "end_label_seq_id": 83
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "DNA-binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "beg_label_seq_id": 84,
+            "end_label_seq_id": 231
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Acyl-CoA\nbinding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "B",
+            "beg_label_seq_id": 84,
+            "end_label_seq_id": 231
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Acyl-CoA binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "C"
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "DNA X"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "D"
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "DNA Y"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "D",
+            "atom_id": 4016
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "DNA Y O5'"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "D",
+            "atom_id": 4391
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "DNA Y O3'"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "E"
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Gold"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "H"
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Gold"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "F"
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Chloride"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "G"
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Chloride"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "I"
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Chloride"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "label_seq_id": 57
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "label_seq_id": 67
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "label_seq_id": 121
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "label_seq_id": 125
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "label_seq_id": 129
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "label_seq_id": 178
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "A",
+            "beg_label_seq_id": 203,
+            "end_label_seq_id": 205
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "B",
+            "label_seq_id": 67
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "B",
+            "label_seq_id": 121
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "B",
+            "label_seq_id": 125
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "B",
+            "label_seq_id": 129
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "B",
+            "label_seq_id": 178
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": {
+            "label_asym_id": "B",
+            "beg_label_seq_id": 203,
+            "end_label_seq_id": 205
+           }
+          },
+          "children": [
+           {
+            "kind": "label",
+            "params": {
+             "text": "Ligand binding"
+            }
+           }
+          ]
+         },
+         {
+          "kind": "component",
+          "params": {
+           "selector": "all"
+          },
+          "children": [
+           {
+            "kind": "focus",
+            "params": {
+             "direction": [-0.3, -0.1, -1]
+            }
+           }
+          ]
+         }
+        ]
+       }
+      ]
+     }
+    ]
+   },
+   {
+    "kind": "canvas",
+    "params": {
+     "background_color": "#eeffee"
+    }
+   }
+  ]
+ }
+}

examples/mvs/1h9t_domains.json

@@ -0,0 +1,155 @@
+[
+    {
+        "label_asym_id": "A",
+        "beg_label_seq_id": 9,
+        "end_label_seq_id": 83,
+        "color": "#dd6600",
+        "tooltip": "DNA-binding"
+    },
+    {
+        "label_asym_id": "A",
+        "beg_label_seq_id": 84,
+        "end_label_seq_id": 231,
+        "color": "#008800",
+        "tooltip": "Acyl-CoA binding"
+    },
+    {
+        "label_asym_id": "B",
+        "beg_label_seq_id": 9,
+        "end_label_seq_id": 83,
+        "color": "#cc8800",
+        "tooltip": "DNA-binding"
+    },
+    {
+        "label_asym_id": "B",
+        "beg_label_seq_id": 84,
+        "end_label_seq_id": 231,
+        "color": "#008888",
+        "tooltip": "Acyl-CoA binding"
+    },
+    {
+        "label_asym_id": "C",
+        "color": "#1100aa",
+        "tooltip": "DNA X"
+    },
+    {
+        "label_asym_id": "D",
+        "color": "#dddddd",
+        "tooltip": "DNA Y"
+    },
+    {
+        "label_asym_id": "D",
+        "atom_id": 4016,
+        "color": "#ff0044",
+        "tooltip": "DNA Y - O5'"
+    },
+    {
+        "label_asym_id": "D",
+        "atom_id": 4391,
+        "color": "#4400ff",
+        "tooltip": "DNA Y - O3'"
+    },
+    
+
+    {
+        "label_asym_id": "E",
+        "color": "#ffff00",
+        "tooltip": "Gold"
+    },
+    {
+        "label_asym_id": "H",
+        "color": "#ffff00",
+        "tooltip": "Gold"
+    },
+    {
+        "label_asym_id": "F",
+        "color": "#00dd00",
+        "tooltip": "Chloride"
+    },
+    {
+        "label_asym_id": "G",
+        "color": "#00dd00",
+        "tooltip": "Chloride"
+    },
+    {
+        "label_asym_id": "I",
+        "color": "#00dd00",
+        "tooltip": "Chloride"
+    },
+
+    {
+        "label_asym_id": "A",
+        "label_seq_id": 57,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "A",
+        "label_seq_id": 67,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "A",
+        "label_seq_id": 121,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "A",
+        "label_seq_id": 125,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "A",
+        "label_seq_id": 129,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "A",
+        "label_seq_id": 178,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "A",
+        "beg_label_seq_id": 203,
+        "end_label_seq_id": 205,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+
+    {
+        "label_asym_id": "B",
+        "label_seq_id": 67,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "B",
+        "label_seq_id": 121,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "B",
+        "label_seq_id": 125,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "B",
+        "label_seq_id": 129,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    },
+    {
+        "label_asym_id": "B",
+        "beg_label_seq_id": 203,
+        "end_label_seq_id": 205,
+        "color": "#ff0000",
+        "tooltip": "Ligand binding site"
+    }
+]

examples/trajectory/protein.parm7

@@ -0,0 +1,264 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 11/04/25  11:55:47
+%FLAG TITLE
+%FORMAT(20a4)
+alanine-dipeptide.solvated.pdb  
+%FLAG POINTERS
+%FORMAT(10I8)
+      22       7      12       9      25      11      39      19       0       0
+      99       3       9      11      19       7      11      20       0       0
+       0       0       0       0       0       0       0       1      10       0
+       0       1
+%FLAG ATOM_NAME
+%FORMAT(20a4)
+H1  CH3 H2  H3  C   O   N   H   CA  HA  CB  HB1 HB2 HB3 C   O   N   H   C   H1  
+H2  H3  
+%FLAG ATOMIC_NUMBER
+%FORMAT(10I8)
+       1       6       1       1       6       8       7       1       6       1
+       6       1       1       1       6       8       7       1       6       1
+       1       1
+%FLAG RESIDUE_LABEL
+%FORMAT(20a4)
+ACE ALA NME 
+%FLAG RESIDUE_POINTER
+%FORMAT(10I8)
+       1       7      17
+%FLAG RESIDUE_NUMBER
+%FORMAT(20I4)
+   1   2   3
+%FLAG RESIDUE_ICODE
+%FORMAT(20a4)
+            
+%FLAG RESIDUE_CHAINID
+%FORMAT(20a4)
+B   B   B   
+%FLAG SOLVENT_POINTERS
+%FORMAT(3I8)
+       0       1       0
+%FLAG ATOMS_PER_MOLECULE
+%FORMAT(10I8)
+      22
+%FLAG MASS
+%FORMAT(5E16.8)
+  3.02400000E+00  5.96200000E+00  3.02400000E+00  3.02400000E+00  1.20100000E+01
+  1.60000000E+01  1.19940000E+01  3.02400000E+00  9.99400000E+00  3.02400000E+00
+  5.96200000E+00  3.02400000E+00  3.02400000E+00  3.02400000E+00  1.20100000E+01
+  1.60000000E+01  1.19940000E+01  3.02400000E+00  5.96200000E+00  3.02400000E+00
+  3.02400000E+00  3.02400000E+00
+%FLAG CHARGE
+%FORMAT(5E16.8)
+  2.04636429E+00 -6.67300626E+00  2.04636429E+00  2.04636429E+00  1.08823576E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00  6.14091510E-01  1.49969529E+00
+ -3.32556975E+00  1.09880469E+00  1.09880469E+00  1.09880469E+00  1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00  4.95464337E+00 -2.71512270E+00  1.77849648E+00
+  1.77849648E+00  1.77849648E+00
+%FLAG AMBER_ATOM_TYPE
+%FORMAT(20a4)
+a0  a1  a0  a0  a2  a3  a4  a5  a1  a6  a1  a0  a0  a0  a2  a3  a4  a5  a1  a6  
+a6  a6  
+%FLAG ATOM_TYPE_INDEX
+%FORMAT(10I8)
+       1       2       1       1       3       4       5       6       2       7
+       2       1       1       1       3       4       5       6       2       7
+       7       7
+%FLAG NONBONDED_PARM_INDEX
+%FORMAT(10I8)
+       1       2       4       7      11      16      22       2       3       5
+       8      12      17      23       4       5       6       9      13      18
+      24       7       8       9      10      14      19      25      11      12
+      13      14      15      20      26      16      17      18      19      20
+      21      27      22      23      24      25      26      27      28
+%FLAG LENNARD_JONES_ACOEF
+%FORMAT(5E16.8)
+  7.51607703E+03  9.71708117E+04  1.04308023E+06  8.61541883E+04  9.24822269E+05
+  8.19971662E+05  5.44261042E+04  6.47841732E+05  5.74393458E+05  3.79876399E+05
+  8.96776989E+04  9.95480466E+05  8.82619071E+05  6.06829343E+05  9.44293233E+05
+  1.07193645E+02  2.56678134E+03  2.27577560E+03  1.02595236E+03  2.12601181E+03
+  1.39982777E-01  4.98586847E+03  6.78771368E+04  6.01816484E+04  3.69471530E+04
+  6.20665998E+04  5.94667299E+01  3.25969625E+03
+%FLAG LENNARD_JONES_BCOEF
+%FORMAT(5E16.8)
+  2.17257828E+01  1.26919150E+02  6.75612247E+02  1.12529845E+02  5.99015525E+02
+  5.31102864E+02  1.11805549E+02  6.26720080E+02  5.55666449E+02  5.64885984E+02
+  1.36131731E+02  7.36907417E+02  6.53361429E+02  6.77220874E+02  8.01323529E+02
+  2.59456373E+00  2.06278363E+01  1.82891803E+01  1.53505284E+01  2.09604198E+01
+  9.37598976E-02  1.76949863E+01  1.06076943E+02  9.40505981E+01  9.21192137E+01
+  1.13252062E+02  1.93248820E+00  1.43076527E+01
+%FLAG NUMBER_EXCLUDED_ATOMS
+%FORMAT(10I8)
+       6       7       4       3       7       3      10       4      10       7
+       6       3       2       1       7       3       5       4       3       2
+       1       1
+%FLAG EXCLUDED_ATOMS_LIST
+%FORMAT(10I8)
+       2       3       4       5       6       7       3       4       5       6
+       7       8       9       4       5       6       7       5       6       7
+       6       7       8       9      10      11      15       7       8       9
+       8       9      10      11      12      13      14      15      16      17
+       9      10      11      15      10      11      12      13      14      15
+      16      17      18      19      11      12      13      14      15      16
+      17      12      13      14      15      16      17      13      14      15
+      14      15      15      16      17      18      19      20      21      22
+      17      18      19      18      19      20      21      22      19      20
+      21      22      20      21      22      21      22      22       0
+%FLAG BOND_FORCE_CONSTANT
+%FORMAT(5E16.8)
+  3.40000000E+02  4.34000000E+02  3.17000000E+02  5.70000000E+02  4.90000000E+02
+  3.37000000E+02  3.10000000E+02
+%FLAG BOND_EQUIL_VALUE
+%FORMAT(5E16.8)
+  1.09000000E+00  1.01000000E+00  1.52200000E+00  1.22900000E+00  1.33500000E+00
+  1.44900000E+00  1.52600000E+00
+%FLAG BONDS_INC_HYDROGEN
+%FORMAT(10I8)
+       0       3       1       3       6       1       3       9       1      18
+      21       2      24      27       1      30      33       1      30      36
+       1      30      39       1      48      51       2      54      57       1
+      54      60       1      54      63       1
+%FLAG BONDS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+       3      12       3      12      15       4      12      18       5      18
+      24       6      24      42       3      24      30       7      42      48
+       5      42      45       4      48      54       6
+%FLAG ANGLE_FORCE_CONSTANT
+%FORMAT(5E16.8)
+  3.50000000E+01  5.00000000E+01  5.00000000E+01  5.00000000E+01  8.00000000E+01
+  7.00000000E+01  5.00000000E+01  8.00000000E+01  8.00000000E+01  6.30000000E+01
+  6.30000000E+01
+%FLAG ANGLE_EQUIL_VALUE
+%FORMAT(5E16.8)
+  1.91113553E+00  1.91113553E+00  2.09439510E+00  2.06018665E+00  2.10137642E+00
+  2.03505391E+00  2.12755636E+00  2.14500965E+00  1.91462619E+00  1.92160751E+00
+  1.93906080E+00
+%FLAG ANGLES_INC_HYDROGEN
+%FORMAT(10I8)
+       0       3       6       1       0       3       9       1       0       3
+      12       2       6       3       9       1       6       3      12       2
+       9       3      12       2      12      18      21       3      18      24
+      27       2      21      18      24       4      24      30      33       2
+      24      30      36       2      24      30      39       2      27      24
+      30       2      27      24      42       2      33      30      36       1
+      33      30      39       1      36      30      39       1      42      48
+      51       3      48      54      57       2      48      54      60       2
+      48      54      63       2      51      48      54       4      57      54
+      60       1      57      54      63       1      60      54      63       1
+%FLAG ANGLES_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+       3      12      15       5       3      12      18       6      12      18
+      24       7      15      12      18       8      18      24      30       9
+      18      24      42      10      24      42      45       5      24      42
+      48       6      30      24      42      11      42      48      54       7
+      45      42      48       8
+%FLAG DIHEDRAL_FORCE_CONSTANT
+%FORMAT(5E16.8)
+  8.00000000E-01  8.00000000E-02  2.50000000E+00  2.50000000E+00  2.00000000E+00
+  1.55555556E-01  1.10000000E+00  0.00000000E+00  0.00000000E+00  8.00000000E-01
+  1.80000000E+00  4.20000000E-01  2.70000000E-01  5.50000000E-01  1.58000000E+00
+  4.50000000E-01  4.00000000E-01  2.00000000E-01  2.00000000E-01  1.05000000E+01
+%FLAG DIHEDRAL_PERIODICITY
+%FORMAT(5E16.8)
+  1.00000000E+00  3.00000000E+00  2.00000000E+00  2.00000000E+00  1.00000000E+00
+  3.00000000E+00  2.00000000E+00  1.00000000E+00  1.00000000E+00  3.00000000E+00
+  2.00000000E+00  3.00000000E+00  2.00000000E+00  3.00000000E+00  2.00000000E+00
+  1.00000000E+00  3.00000000E+00  2.00000000E+00  1.00000000E+00  2.00000000E+00
+%FLAG DIHEDRAL_PHASE
+%FORMAT(5E16.8)
+  0.00000000E+00  3.14159265E+00  3.14159265E+00  3.14159265E+00  0.00000000E+00
+  0.00000000E+00  3.14159265E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00  3.14159265E+00
+  3.14159265E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  3.14159265E+00
+%FLAG SCEE_SCALE_FACTOR
+%FORMAT(5E16.8)
+  1.20000000E+00  0.00000000E+00  1.20000000E+00  1.20000000E+00  0.00000000E+00
+  1.20000000E+00  0.00000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
+  0.00000000E+00  1.20000000E+00  0.00000000E+00  1.20000000E+00  0.00000000E+00
+  0.00000000E+00  1.20000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG SCNB_SCALE_FACTOR
+%FORMAT(5E16.8)
+  2.00000000E+00  0.00000000E+00  2.00000000E+00  2.00000000E+00  0.00000000E+00
+  2.00000000E+00  0.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
+  0.00000000E+00  2.00000000E+00  0.00000000E+00  2.00000000E+00  0.00000000E+00
+  0.00000000E+00  2.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG DIHEDRALS_INC_HYDROGEN
+%FORMAT(10I8)
+       0       3      12      15       1       0       3     -12      15       2
+       3      12      18      21       3       6       3      12      15       1
+       6       3     -12      15       2       9       3      12      15       1
+       9       3     -12      15       2      15      12      18      21       4
+      15      12     -18      21       5      18      24      30      33       6
+      18      24      30      36       6      18      24      30      39       6
+      24      42      48      51       3      27      24      30      33       6
+      27      24      30      36       6      27      24      30      39       6
+      27      24      42      45       1      27      24     -42      45       2
+      42      24      30      33       6      42      24      30      36       6
+      42      24      30      39       6      45      42      48      51       4
+      45      42     -48      51       5      21      18     -24     -12       7
+      51      48     -54     -42       7      51      48      54      60       8
+      21      18      24      30       8      42      48      54      57       8
+       6       3      12      18       9      42      48      54      63       8
+      51      48      54      57       8      21      18      24      42       8
+       0       3      12      18       9      42      48      54      60       8
+      27      24      42      48       8      21      18      24      27       8
+      51      48      54      63       8       9       3      12      18       9
+      12      18      24      27       8
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+       3      12      18      24       3      12      18      24      30      10
+      12      18     -24      30      11      12      18     -24      30       5
+      12      18      24      42      12      12      18     -24      42      13
+      15      12      18      24       3      18      24      42      48      14
+      18      24     -42      48      15      18      24     -42      48      16
+      24      42      48      54       3      30      24      42      48      17
+      30      24     -42      48      18      30      24     -42      48      19
+      45      42      48      54       3      15      12     -18      -3      20
+      45      42     -48     -24      20      18      24      42      45       8
+      30      24      42      45       8
+%FLAG SOLTY
+%FORMAT(5E16.8)
+
+%FLAG HBOND_ACOEF
+%FORMAT(5E16.8)
+
+%FLAG HBOND_BCOEF
+%FORMAT(5E16.8)
+
+%FLAG HBCUT
+%FORMAT(5E16.8)
+
+%FLAG TREE_CHAIN_CLASSIFICATION
+%FORMAT(20a4)
+BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
+BLA BLA 
+%FLAG JOIN_ARRAY
+%FORMAT(10I8)
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0
+%FLAG IROTAT
+%FORMAT(10I8)
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0
+%FLAG BOX_DIMENSIONS
+%FORMAT(5E16.8)
+  9.00000000E+01  3.00000000E+01  3.00000000E+01  3.00000000E+01
+%FLAG RADIUS_SET
+%FORMAT(1a80)
+0                                                                               
+%FLAG RADII
+%FORMAT(5E16.8)
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00
+%FLAG SCREEN
+%FORMAT(5E16.8)
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00
+%FLAG IPOL
+%FORMAT(1I8)
+       0

examples/trajectory/protein.pdb

@@ -0,0 +1,26 @@
+CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1           1
+ATOM      1  H1  ACE A   1       2.000   1.000  -0.000  0.00  0.00           H  
+ATOM      2  CH3 ACE A   1       2.000   2.090   0.000  0.00  0.00           C  
+ATOM      3  H2  ACE A   1       1.486   2.454   0.890  0.00  0.00           H  
+ATOM      4  H3  ACE A   1       1.486   2.454  -0.890  0.00  0.00           H  
+ATOM      5  C   ACE A   1       3.427   2.641  -0.000  0.00  0.00           C  
+ATOM      6  O   ACE A   1       4.391   1.877  -0.000  0.00  0.00           O  
+ATOM      7  N   ALA A   2       3.555   3.970  -0.000  0.00  0.00           N  
+ATOM      8  H   ALA A   2       2.733   4.556  -0.000  0.00  0.00           H  
+ATOM      9  CA  ALA A   2       4.853   4.614  -0.000  0.00  0.00           C  
+ATOM     10  HA  ALA A   2       5.408   4.316   0.890  0.00  0.00           H  
+ATOM     11  CB  ALA A   2       5.661   4.221  -1.232  0.00  0.00           C  
+ATOM     12  HB1 ALA A   2       5.123   4.521  -2.131  0.00  0.00           H  
+ATOM     13  HB2 ALA A   2       6.630   4.719  -1.206  0.00  0.00           H  
+ATOM     14  HB3 ALA A   2       5.809   3.141  -1.241  0.00  0.00           H  
+ATOM     15  C   ALA A   2       4.713   6.129   0.000  0.00  0.00           C  
+ATOM     16  O   ALA A   2       3.601   6.653   0.000  0.00  0.00           O  
+ATOM     17  N   NME A   3       5.846   6.835   0.000  0.00  0.00           N  
+ATOM     18  H   NME A   3       6.737   6.359  -0.000  0.00  0.00           H  
+ATOM     19  C   NME A   3       5.846   8.284   0.000  0.00  0.00           C  
+ATOM     20  H1  NME A   3       4.819   8.648   0.000  0.00  0.00           H  
+ATOM     21  H2  NME A   3       6.360   8.648   0.890  0.00  0.00           H  
+ATOM     22  H3  NME A   3       6.360   8.648  -0.890  0.00  0.00           H  
+TER      23      NME A   3 
+CONECT    5    7
+CONECT   15   17

examples/trajectory/protein.rst7

@@ -0,0 +1,14 @@
+alanine-dipeptide.solvated.pdb
+    22
+   0.7494821   1.2436848   0.8743532   1.0856344   2.2423820   0.5955986
+   0.4304414   2.9747953   1.0671825   1.0497815   2.3544810  -0.4880289
+   2.5015950   2.4471725   1.0820421   3.1003812   1.5343071   1.6479120
+   3.0220696   3.6519467   0.8741013   2.4411554   4.3533213   0.4373955
+   4.3920715   4.0500473   1.2160543   4.7674596   3.4172266   2.0202454
+   5.2805058   3.8202998  -0.0180103   4.9565949   4.4537317  -0.8438106
+   6.3180425   4.0583459   0.2164072   5.2327259   2.7740601  -0.3200050
+   4.4431625   5.5106563   1.7135265   3.4307644   6.2198007   1.6891606
+   5.6170320   5.9613562   2.1744082   6.3997462   5.3231585   2.1616313
+   5.8784762   7.3296314   2.6320299   5.1056278   8.0184146   2.2908769
+   5.9253575   7.3544224   3.7207393   6.8360338   7.6745804   2.2419090
+  30.0000000  30.0000000  30.0000000  90.0000000  90.0000000  90.0000000

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.2.0",
+  "version": "5.9.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -10,29 +10,30 @@
   "bugs": {
     "url": "https://github.com/molstar/molstar/issues"
   },
+  "engines": {
+    "node": ">=22.0.0"
+  },
   "scripts": {
     "lint": "eslint .",
     "lint-fix": "eslint . --fix",
-    "test": "npm install --no-save \"gl@^5.0.0\" && npm run lint && jest",
+    "test": "npm install --no-save \"gl@^6.0.2\" && npm run lint && jest",
     "jest": "jest",
-    "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
-    "clean": "node ./scripts/clean.js",
+    "clean": "node ./scripts/clean.js --all",
+    "clean:build": "node ./scripts/clean.js --build",
+    "build": "npm run build:apps && npm run build:lib",
+    "build:apps": "node ./scripts/build.mjs -a -e --prd",
+    "build:lib": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\" && npm run build:lib-extra",
+    "build:lib-extra": "node scripts/write-version.mjs && cpx \"src/**/*.{scss,html,ico,jpg}\" lib/ && cpx \"src/**/*.{scss,html,ico,jpg}\" lib/commonjs/ && tsc-alias -p tsconfig.json",
     "rebuild": "npm run clean && npm run build",
-    "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
-    "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",
-    "build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
-    "build-webpack": "webpack --mode production --config ./webpack.config.production.js",
-    "build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
-    "watch": "concurrently -c \"green,green,gray,gray\" --names \"tsc,srv,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-servers\" \"npm:watch-extra\" \"npm:watch-webpack\"",
-    "watch-viewer": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer\"",
-    "watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
-    "watch-tsc": "tsc --watch --incremental",
-    "watch-servers": "tsc --build tsconfig.commonjs.json --watch --incremental",
-    "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
-    "watch-webpack": "webpack -w --mode development --stats minimal",
-    "watch-webpack-viewer": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.js",
-    "watch-webpack-viewer-debug": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.debug.js",
+    "dev": "node ./scripts/build.mjs",
+    "dev:all": "node ./scripts/build.mjs -a -e -bt",
+    "dev:viewer": "node ./scripts/build.mjs -a viewer",
+    "dev:apps": "node ./scripts/build.mjs -a",
+    "dev:examples": "node ./scripts/build.mjs -e",
+    "dev:browser-tests": "node ./scripts/build.mjs -bt",
     "serve": "http-server -p 1338 -g",
+    "deploy:local": "npm run clean:build && npm run build:apps && node ./scripts/deploy.js --local",
+    "deploy:remote": "npm run clean:build && npm run build:apps && node ./scripts/deploy.js",
     "model-server": "node lib/commonjs/servers/model/server.js",
     "model-server-watch": "nodemon --watch lib lib/commonjs/servers/model/server.js",
     "volume-server-test": "node lib/commonjs/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
@@ -43,11 +44,15 @@
   },
   "files": [
     "lib/",
-    "build/viewer/"
+    "build/viewer/",
+    "build/mvs-stories/"
   ],
   "bin": {
     "cif2bcif": "lib/commonjs/cli/cif2bcif/index.js",
     "cifschema": "lib/commonjs/cli/cifschema/index.js",
+    "mvs-validate": "lib/commonjs/cli/mvs/mvs-validate.js",
+    "mvs-render": "lib/commonjs/cli/mvs/mvs-render.js",
+    "mvs-print-schema": "lib/commonjs/cli/mvs/mvs-print-schema.js",
     "model-server": "lib/commonjs/servers/model/server.js",
     "model-server-query": "lib/commonjs/servers/model/query.js",
     "model-server-preprocess": "lib/commonjs/servers/model/preprocess.js",
@@ -69,13 +74,15 @@
       "js"
     ],
     "transform": {
-      "\\.ts$": "ts-jest"
+      "\\.ts$": ["esbuild-jest-transform", { "tsconfigRaw": "{\"compilerOptions\":{\"useDefineForClassFields\":false}}" }]
     },
     "moduleDirectories": [
       "node_modules",
       "lib"
     ],
-    "testURL": "http://localhost/",
+    "testEnvironmentOptions": {
+      "url": "http://localhost/"
+    },
     "testRegex": "\\.spec\\.ts$"
   },
   "author": "Mol* Contributors",
@@ -87,74 +94,115 @@
     "Ludovic Autin <autin@scripps.edu>",
     "Michal Malý <michal.maly@ibt.cas.cz>",
     "Jiří Černý <jiri.cerny@ibt.cas.cz>",
-    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>"
+    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>",
+    "Adam Midlik <midlik@gmail.com>",
+    "Koya Sakuma <koya.sakuma.work@gmail.com>",
+    "Gianluca Tomasello <giagitom@gmail.com>",
+    "Ke Ma <mark.ma@rcsb.org>",
+    "Jason Pattle <jpattle@exscientia.co.uk>",
+    "David Williams <dwilliams@nobiastx.com>",
+    "Zhenyu Zhang <jump2cn@gmail.com>",
+    "Russell Parker <russell@benchling.com>",
+    "Dominik Tichy <tichydominik451@gmail.com>",
+    "Yana Rose <yana.v.rose@gmail.com>",
+    "Yakov Pechersky <ffxen158@gmail.com>",
+    "Christian Dominguez <christian.99dominguez@gmail.com>",
+    "Cai Huiyu <szmun.caihy@gmail.com>",
+    "Ryan DiRisio <rjdiris@gmail.com>",
+    "Dušan Veľký <dvelky@mail.muni.cz>",
+    "Neli Fonseca <neli@ebi.ac.uk>",
+    "Paul Pillot <paul.pillot@tandemai.com>",
+    "Herman Bergwerf <post@hbergwerf.nl>",
+    "Eric E <etongfu@outlook.com>",
+    "Xavier Martinez <xavier.martinez.xm@gmail.com>",
+    "Alex Chan <smalldirkalex@gmail.com>",
+    "Simeon Borko <simeon.borko@gmail.com>",
+    "Ventura Rivera <venturaxrivera@gmail.com>",
+    "Andy Turner <agdturner@gmail.com>",
+    "Lukáš Polák <admin@lukaspolak.cz>",
+    "Chetan Mishra <chetan.s115@gmail.com>",
+    "Zach Charlop-Powers <zach.charlop.powers@gmail.com>",
+    "Kim Juho <juho_kim@outlook.com>",
+    "Victoria Doshchenko <doshchenko.victoria@gmail.com>",
+    "Diego del Alamo <diego.delalamo@gmail.com>",
+    "Tianzhen Lin (Tangent) <tangent@usa.net>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.5.0",
-    "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.3",
-    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.3.4",
-    "@graphql-codegen/typescript-operations": "^2.2.4",
-    "@types/cors": "^2.8.12",
-    "@types/gl": "^4.1.0",
-    "@types/jest": "^27.4.0",
-    "@typescript-eslint/eslint-plugin": "^5.10.2",
-    "@typescript-eslint/parser": "^5.10.2",
+    "@types/cors": "^2.8.19",
+    "@types/gl": "^6.0.5",
+    "@types/jest": "^30.0.0",
+    "@types/pngjs": "^6.0.5",
+    "@types/react": "^18.3.28",
+    "@types/react-dom": "^18.3.7",
+    "@types/webxr": "^0.5.24",
+    "@typescript-eslint/eslint-plugin": "^8.59.1",
+    "@typescript-eslint/parser": "^8.59.1",
     "benchmark": "^2.1.4",
-    "concurrently": "^7.0.0",
-    "cpx2": "^4.1.2",
-    "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.6.0",
-    "eslint": "^8.8.0",
-    "extra-watch-webpack-plugin": "^1.0.3",
-    "file-loader": "^6.2.0",
-    "fs-extra": "^10.0.0",
-    "graphql": "^16.3.0",
-    "http-server": "^14.1.0",
-    "jest": "^27.5.0",
-    "mini-css-extract-plugin": "^2.5.3",
-    "path-browserify": "^1.0.1",
-    "raw-loader": "^4.0.2",
-    "sass": "^1.49.7",
-    "sass-loader": "^12.4.0",
-    "simple-git": "^3.1.1",
-    "stream-browserify": "^3.0.0",
-    "style-loader": "^3.3.1",
-    "ts-jest": "^27.1.3",
-    "typescript": "^4.5.5",
-    "webpack": "^5.68.0",
-    "webpack-cli": "^4.9.2"
+    "concurrently": "^9.2.1",
+    "cpx2": "^8.0.2",
+    "css-loader": "^7.1.4",
+    "esbuild": "^0.28.0",
+    "esbuild-jest-transform": "^2.0.1",
+    "esbuild-sass-plugin": "^3.7.0",
+    "eslint": "^10.3.0",
+    "fs-extra": "^11.3.4",
+    "globals": "^17.6.0",
+    "http-server": "^14.1.1",
+    "jest": "^30.3.0",
+    "jpeg-js": "^0.4.4",
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1",
+    "sass": "^1.99.0",
+    "simple-git": "^3.36.0",
+    "tsc-alias": "^1.8.17",
+    "typescript": "^6.0.3"
   },
   "dependencies": {
-    "@types/argparse": "^2.0.10",
-    "@types/benchmark": "^2.1.1",
-    "@types/compression": "1.7.2",
-    "@types/express": "^4.17.13",
-    "@types/node": "^16.11.22",
-    "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.39",
-    "@types/react-dom": "^17.0.11",
-    "@types/swagger-ui-dist": "3.30.1",
+    "@types/argparse": "^2.0.17",
+    "@types/benchmark": "^2.1.5",
+    "@types/compression": "1.8.1",
+    "@types/express": "^5.0.6",
+    "@types/node": "^22.19.17",
+    "@types/swagger-ui-dist": "3.30.6",
     "argparse": "^2.0.1",
-    "body-parser": "^1.19.1",
-    "compression": "^1.7.4",
-    "cors": "^2.8.5",
-    "express": "^4.17.2",
+    "compression": "^1.8.1",
+    "cors": "^2.8.6",
+    "express": "^5.2.1",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.12",
-    "immutable": "^4.0.0",
-    "node-fetch": "^2.6.7",
-    "rxjs": "^7.5.2",
-    "swagger-ui-dist": "^4.5.0",
-    "tslib": "^2.3.1",
-    "util.promisify": "^1.1.1",
-    "xhr2": "^0.2.1"
+    "immutable": "^5.1.5",
+    "io-ts": "^2.2.22",
+    "mutative": "^1.3.0",
+    "react-markdown": "^10.1.0",
+    "remark-gfm": "^4.0.1",
+    "rxjs": "^7.8.2",
+    "swagger-ui-dist": "^5.32.5",
+    "tslib": "^2.8.1"
   },
   "peerDependencies": {
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2"
+    "@google-cloud/storage": "^7.14.0",
+    "canvas": "^2.11.2",
+    "gl": "^6.0.2",
+    "jpeg-js": "^0.4.4",
+    "pngjs": "^6.0.0",
+    "react": ">=16.14.0",
+    "react-dom": ">=16.14.0"
+  },
+  "peerDependenciesMeta": {
+    "@google-cloud/storage": {
+      "optional": true
+    },
+    "canvas": {
+      "optional": true
+    },
+    "gl": {
+      "optional": true
+    },
+    "jpeg-js": {
+      "optional": true
+    },
+    "pngjs": {
+      "optional": true
+    }
   }
 }

scripts/build.mjs

@@ -0,0 +1,350 @@
+/**
+ * Copyright (c) 2017-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Eric E <etongfu@@outlook.com>
+ */
+import * as esbuild from 'esbuild';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as argparse from 'argparse';
+import { sassPlugin } from 'esbuild-sass-plugin';
+import * as os from 'os';
+
+const Apps = [
+    // Apps
+    { kind: 'app', name: 'viewer', themes: ['light', 'dark', 'blue'] },
+    { kind: 'app', name: 'docking-viewer' },
+    { kind: 'app', name: 'mesoscale-explorer' },
+    { kind: 'app', name: 'mvs-stories', globalName: 'mvsStories', filename: 'mvs-stories.js' },
+
+    // Examples
+    { kind: 'example', name: 'proteopedia-wrapper' },
+    { kind: 'example', name: 'basic-wrapper' },
+    { kind: 'example', name: 'lighting' },
+    { kind: 'example', name: 'alpha-orbitals' },
+    { kind: 'example', name: 'alphafolddb-pae' },
+    { kind: 'example', name: 'mvs-stories' },
+    { kind: 'example', name: 'ihm-restraints' },
+    { kind: 'example', name: 'interactions' },
+    { kind: 'example', name: 'ligand-editor' },
+];
+
+function findApp(name, kind) {
+    return Apps.find(a => a.name === name && a.kind === kind);
+}
+
+function mkDir(dir) {
+    try {
+        if (!fs.existsSync(dir)) {
+            fs.mkdirSync(dir, { recursive: true });
+        }
+    } catch (error) {
+        console.error(`Failed to create directory ${dir}:`, error);
+        process.exit(1);
+    }
+}
+
+function handleFileError(error, operation, path) {
+    console.error(`Failed to ${operation} ${path}:`, error);
+    process.exit(1);
+}
+
+function fileLoaderPlugin(options) {
+    mkDir(options.out);
+
+    return {
+        name: 'file-loader',
+        setup(build) {
+            build.onLoad({ filter: /\.jpg$/ }, async (args) => {
+                try {
+                    const name = path.basename(args.path);
+                    mkDir(path.resolve(options.out, 'images'));
+                    await fs.promises.copyFile(args.path, path.resolve(options.out, 'images', name));
+                    return {
+                        contents: `images/${name}`,
+                        loader: 'text',
+                    };
+                } catch (error) {
+                    handleFileError(error, 'copy', args.path);
+                }
+            });
+            build.onLoad({ filter: /\.(html|ico)$/ }, async (args) => {
+                const name = path.basename(args.path);
+                await fs.promises.copyFile(args.path, path.resolve(options.out, name));
+                return {
+                    contents: '',
+                    loader: 'empty',
+                };
+            });
+        },
+    };
+}
+
+function examplesCssRenamePlugin({ root }) {
+    return {
+        name: 'example-css-rename',
+        setup(build) {
+            build.onEnd(async () => {
+                if (fs.existsSync(path.resolve(root, 'index.css'))) {
+                    await fs.promises.rename(
+                        path.resolve(root, 'index.css'),
+                        path.resolve(root, 'molstar.css')
+                    );
+                }
+            });
+        }
+    };
+}
+
+function resolveEntryPath(path) {
+    if (!fs.existsSync(path)) {
+        return path + 'x'; // fallback to .tsx
+    }
+    return path;
+}
+
+function getPaths(app) {
+    if (app.kind === 'app') {
+        return {
+            prefix: `./build/${app.name}`,
+            entry: resolveEntryPath(`./src/apps/${app.name}/index.ts`),
+            outfile: `./build/${app.name}/${app.filename || 'molstar.js'}`,
+        };
+    }
+    if (app.kind === 'example') {
+        return {
+            prefix: `./build/examples/${app.name}`,
+            entry: resolveEntryPath(`./src/examples/${app.name}/index.ts`),
+            outfile: `./build/examples/${app.name}/${app.filename || 'index.js'}`,
+        };
+    }
+    if (app.kind === 'browser-test') {
+        return {
+            prefix: `./build/tests/browser`,
+            entry: resolveEntryPath(`./src/tests/browser/${app.name}.ts`),
+            outfile: `./build/tests/browser/${app.name}.js`,
+        };
+    }
+    throw new Error(`Unknown app kind: ${app.kind}`);
+}
+
+async function createBundle(app) {
+    const { name, kind } = app;
+    const { prefix, entry, outfile } = getPaths(app);
+
+    const ctx = await esbuild.context({
+        entryPoints: [entry],
+        tsconfig: './tsconfig.json',
+        bundle: true,
+        minify: isProduction,
+        minifyIdentifiers: false,
+        sourcemap: includeSourceMap,
+        globalName: app.globalName || 'molstar',
+        outfile,
+        plugins: [
+            fileLoaderPlugin({ out: prefix }),
+            sassPlugin({
+                type: 'css',
+                silenceDeprecations: ['import'],
+                logger: {
+                    warn: (msg) => console.warn(msg),
+                    debug: () => { },
+                }
+            }),
+            ...(kind === 'example' ? [examplesCssRenamePlugin({ root: prefix })] : []),
+        ],
+        external: ['crypto', 'fs', 'path', 'stream'],
+        loader: {
+        },
+        color: true,
+        logLevel: 'info',
+        define: {
+            'process.env.NODE_ENV': JSON.stringify(NODE_ENV_PRD ? 'production' : 'development'),
+            'process.env.DEBUG': JSON.stringify(process.env.DEBUG || false),
+            __MOLSTAR_PLUGIN_VERSION__: JSON.stringify(VERSION),
+            __MOLSTAR_BUILD_TIMESTAMP__: `${TIMESTAMP}`,
+        },
+    });
+
+    await ctx.rebuild();
+
+    if (!isProduction) await ctx.watch();
+}
+
+async function createTheme(appName, themeName) {
+    // const { prefix, entry, outfile } = getPaths(app);
+
+    const ctx = await esbuild.context({
+        entryPoints: [resolveEntryPath(`./src/apps/${appName}/theme/${themeName}.ts`)],
+        tsconfig: './tsconfig.json',
+        bundle: true,
+        minify: isProduction,
+        minifyIdentifiers: false,
+        sourcemap: false,
+        outfile: `./build/${appName}/theme/${themeName}.js`,
+        plugins: [
+            // fileLoaderPlugin({ out: prefix }),
+            sassPlugin({
+                type: 'css',
+                silenceDeprecations: ['import'],
+                logger: {
+                    warn: (msg) => console.warn(msg),
+                    debug: () => { },
+                }
+            }),
+        ],
+        color: true,
+        logLevel: 'info',
+        define: {
+            'process.env.NODE_ENV': JSON.stringify(NODE_ENV_PRD ? 'production' : 'development'),
+            'process.env.DEBUG': JSON.stringify(process.env.DEBUG || false),
+        },
+    });
+
+    await ctx.rebuild();
+
+    if (!isProduction) await ctx.watch();
+}
+
+function findBrowserTests(names) {
+    const dir = path.resolve('./src', 'tests', 'browser');
+    let files = fs.readdirSync(dir).filter(file => file.endsWith('.ts')).map(file => file.replace('.ts', ''));
+    if (names.length) {
+        files = files.filter(file => names.includes(file));
+    }
+    return files.map(name => ({ kind: 'browser-test', name }));
+}
+
+const argParser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Mol* Build'
+});
+argParser.add_argument('--prd', {
+    help: 'Create a production build.',
+    required: false,
+    action: 'store_true',
+});
+argParser.add_argument('--no-src-map', {
+    help: 'Do not include source map.',
+    required: false,
+    action: 'store_true',
+});
+argParser.add_argument('--apps', '-a', {
+    help: 'Apps to build.',
+    required: false,
+    nargs: '*',
+});
+argParser.add_argument('--examples', '-e', {
+    help: 'Examples to build.',
+    required: false,
+    nargs: '*',
+});
+argParser.add_argument('--browser-tests', '-bt', {
+    help: 'Browser Tests to build.',
+    required: false,
+    nargs: '*',
+});
+argParser.add_argument('--port', '-p', {
+    help: 'Port.',
+    required: false,
+    default: 1338,
+    type: 'int',
+});
+
+argParser.add_argument('--host', {
+    help: 'Show all available host addresses.',
+    required: false,
+    action: 'store_true',
+});
+
+const args = argParser.parse_args();
+
+
+const isProduction = !!args.prd;
+const includeSourceMap = !args.no_src_map;
+
+const NODE_ENV_PRD = isProduction || process.env.NODE_ENV === 'production';
+const VERSION = isProduction ? JSON.parse(fs.readFileSync('./package.json', 'utf8')).version : '(dev build)';
+const TIMESTAMP = Date.now();
+
+const apps = (!args.apps ? [] : (args.apps.length ? args.apps.map(a => findApp(a, 'app')).filter(a => a) : Apps.filter(a => a.kind === 'app')));
+const examples = (!args.examples ? [] : (args.examples.length ? args.examples.map(e => findApp(e, 'example')).filter(a => a) : Apps.filter(a => a.kind === 'example')));
+const browserTests = (!args.browser_tests ? [] : findBrowserTests(args.browser_tests));
+
+console.log('Apps:', apps.map(a => a.name));
+console.log('Examples:', examples.map(e => e.name));
+console.log('Browser Tests', browserTests.map(e => e.name));
+console.log('');
+
+function getLocalIPs() {
+    const interfaces = os.networkInterfaces();
+    const ips = [];
+
+    for (const name of Object.keys(interfaces)) {
+        for (const iface of interfaces[name]) {
+            // Skip internal and non-IPv4 addresses
+            if (iface.internal || iface.family !== 'IPv4') continue;
+            ips.push(iface.address);
+        }
+    }
+
+    return ips;
+}
+
+async function main() {
+    const promises = [];
+    console.log(isProduction ? 'Building apps...' : 'Initial build...');
+
+    for (const app of apps) {
+        promises.push(createBundle(app));
+        if (app.themes) {
+            for (const theme of app.themes) {
+                promises.push(createTheme(app.name, theme));
+            }
+        }
+    }
+    for (const example of examples) promises.push(createBundle(example));
+    for (const browserTest of browserTests) promises.push(createBundle(browserTest));
+
+    await Promise.all(promises);
+
+    if (isProduction) {
+        console.log('Done.');
+        process.exit(0);
+    }
+
+    console.log('Initial build complete.');
+
+    const certfile = './dev.pem';
+    const keyfile = './dev-key.pem';
+
+    const sslEnabled = fs.existsSync(certfile) && fs.existsSync(keyfile);
+    const protocol = sslEnabled ? 'https' : 'http';
+
+    const ctx = await esbuild.context({});
+    ctx.serve({
+        servedir: './',
+        port: args.port,
+        host: '0.0.0.0', // Always listen on all interfaces
+        certfile: sslEnabled ? certfile : undefined,
+        keyfile: sslEnabled ? keyfile : undefined,
+    });
+
+    console.log('');
+    console.log(`Server URL: ${protocol}://localhost:${args.port}`);
+    if (args.host) {
+        console.log('Available host addresses:');
+        const ips = getLocalIPs();
+        ips.forEach(ip => console.log(`  ${protocol}://${ip}:${args.port}`));
+    }
+    console.log('');
+    console.log('Watching for changes...');
+    console.log('');
+    console.log('Press Ctrl+C to stop.');
+}
+
+main().catch((err) => {
+    console.error(err);
+    process.exit(1);
+});

scripts/clean.js

@@ -6,6 +6,7 @@
 
 const fs = require('fs');
 const path = require('path');
+const argparse = require('argparse');
 
 function removeDir(dirPath) {
     for (const ent of fs.readdirSync(dirPath)) {
@@ -24,11 +25,29 @@ function remove(entryPath) {
         fs.unlinkSync(entryPath);
 }
 
-const toClean = [
-    path.resolve(__dirname, '../build'),
-    path.resolve(__dirname, '../lib'),
-    path.resolve(__dirname, '../tsconfig.tsbuildinfo'),
-];
+const argParser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Clean Script'
+});
+argParser.add_argument('--build', { required: false, action: 'store_true' });
+argParser.add_argument('--lib', { required: false, action: 'store_true' });
+argParser.add_argument('--all', { required: false, action: 'store_true' });
+const args = argParser.parse_args();
+
+const toClean = [];
+
+if (args.build || args.all) {
+    toClean.push(path.resolve(__dirname, '../build'));
+    toClean.push(path.resolve(__dirname, '../deploy/data'));
+}
+if (args.lib || args.all) {
+    toClean.push(
+        path.resolve(__dirname, '../lib'),
+        path.resolve(__dirname, '../tsconfig.tsbuildinfo'),
+    );
+}
+
+console.log('\n###', 'cleaning', toClean.join(', '));
 
 toClean.forEach(ph => {
     if (fs.existsSync(ph)) {

scripts/deploy.js

@@ -1,21 +1,34 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 const git = require('simple-git');
 const path = require('path');
-const fs = require("fs");
-const fse = require("fs-extra");
+const fs = require('fs');
+const fse = require('fs-extra');
+const argparse = require('argparse');
 
-const remoteUrl = "https://github.com/molstar/molstar.github.io.git";
+const VERSION = require(path.resolve(__dirname, '../package.json')).version;
+const MVS_STORIES_VERSION = require(path.resolve(__dirname, '../src/apps/mvs-stories/version.ts')).VERSION;
+
+const remoteUrl = 'https://github.com/molstar/molstar.github.io.git';
+const dataDir = path.resolve(__dirname, '../data/');
 const buildDir = path.resolve(__dirname, '../build/');
-const deployDir = path.resolve(buildDir, 'deploy/');
-const localPath = path.resolve(deployDir, 'molstar.github.io/');
+const deployDir = path.resolve(__dirname, '../deploy/');
+const localPath = path.resolve(deployDir, 'data/');
+const repositoryPath = path.resolve(deployDir, 'molstar.github.io/');
 
 const analyticsTag = /<!-- __MOLSTAR_ANALYTICS__ -->/g;
-const analyticsCode = `<!-- Cloudflare Web Analytics --><script defer src='https://static.cloudflareinsights.com/beacon.min.js' data-cf-beacon='{"token": "c414cbae2d284ea995171a81e4a3e721"}'></script><!-- End Cloudflare Web Analytics -->`;
+const analyticsCode = `<!-- Cloudflare Web Analytics --><script defer src='https://static.cloudflareinsights.com/beacon.min.js' data-cf-beacon='{"token": "c414cbae2d284ea995171a81e4a3e721"}'></script><!-- End Cloudflare Web Analytics --><iframe src="https://web3dsurvey.com/collector-iframe.html" style="width: 1px; height: 1px;"></iframe>`;
+
+const manifestTag = /<!-- __MOLSTAR_MANIFEST__ -->/g;
+const manifestCode = `<link rel="manifest" href="./manifest.webmanifest">`;
+
+const pwaTag = /<!-- __MOLSTAR_PWA__ -->/g;
+const pwaCode = `<script src='./pwa.js'></script>`;
 
 function log(command, stdout, stderr) {
     if (command) {
@@ -31,30 +44,117 @@ function addAnalytics(path) {
     fs.writeFileSync(path, result, 'utf8');
 }
 
+function addManifest(path) {
+    const data = fs.readFileSync(path, 'utf8');
+    const result = data.replace(manifestTag, manifestCode);
+    fs.writeFileSync(path, result, 'utf8');
+}
+
+function addPwa(path) {
+    const data = fs.readFileSync(path, 'utf8');
+    const result = data.replace(pwaTag, pwaCode);
+    fs.writeFileSync(path, result, 'utf8');
+}
+
+function addVersion(path) {
+    const data = fs.readFileSync(path, 'utf8');
+    const result = data.replace('__MOLSTAR_VERSION__', VERSION);
+    fs.writeFileSync(path, result, 'utf8');
+}
+
 function copyViewer() {
     console.log('\n###', 'copy viewer files');
-    const viewerBuildPath = path.resolve(buildDir, '../build/viewer/');
+    const viewerBuildPath = path.resolve(buildDir, 'viewer/');
     const viewerDeployPath = path.resolve(localPath, 'viewer/');
     fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true });
     addAnalytics(path.resolve(viewerDeployPath, 'index.html'));
+    addManifest(path.resolve(viewerDeployPath, 'index.html'));
+    addPwa(path.resolve(viewerDeployPath, 'index.html'));
+
+    const pwaDataPath = path.resolve(dataDir, 'pwa/');
+    fse.copySync(pwaDataPath, viewerDeployPath, { overwrite: true });
+    addVersion(path.resolve(viewerDeployPath, 'sw.js'));
+}
+
+function copyMe() {
+    console.log('\n###', 'copy me files');
+    const meBuildPath = path.resolve(buildDir, 'mesoscale-explorer/');
+    const meDeployPath = path.resolve(localPath, 'me/viewer/');
+    fse.copySync(meBuildPath, meDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(meDeployPath, 'index.html'));
+}
+
+function copyMVSStories() {
+    console.log('\n###', 'copy MVS stories files');
+    const mvsStoriesBuildPath = path.resolve(buildDir, 'mvs-stories/');
+    const mvsStoriesDeployPath = path.resolve(localPath, `stories-viewer/v${MVS_STORIES_VERSION}/`);
+    fse.copySync(mvsStoriesBuildPath, mvsStoriesDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(mvsStoriesDeployPath, 'index.html'));
+
+    // TODO: add PWA
+    // addManifest(path.resolve(mvsStoriesDeployPath, 'index.html'));
+    // addPwa(path.resolve(mvsStoriesDeployPath, 'index.html'));
+}
+
+function copyDemo(name) {
+    console.log('\n###', `copy demo files for ${name}`);
+    const demoBuildPath = path.resolve(buildDir, `examples/${name}/`);
+    const demoDeployPath = path.resolve(localPath, `demos/${name}/`);
+    fse.copySync(demoBuildPath, demoDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(demoDeployPath, 'index.html'));
 }
 
 function copyDemos() {
     console.log('\n###', 'copy demos files');
-    const lightingBuildPath = path.resolve(buildDir, '../build/examples/lighting/');
-    const lightingDeployPath = path.resolve(localPath, 'demos/lighting/');
-    fse.copySync(lightingBuildPath, lightingDeployPath, { overwrite: true });
-    addAnalytics(path.resolve(lightingDeployPath, 'index.html'));
-
-    const orbitalsBuildPath = path.resolve(buildDir, '../build/examples/alpha-orbitals/');
-    const orbitalsDeployPath = path.resolve(localPath, 'demos/alpha-orbitals/');
-    fse.copySync(orbitalsBuildPath, orbitalsDeployPath, { overwrite: true });
-    addAnalytics(path.resolve(orbitalsDeployPath, 'index.html'));
+    copyDemo('lighting');
+    copyDemo('alpha-orbitals');
+    copyDemo('mvs-stories');
 }
 
 function copyFiles() {
-    copyViewer();
-    copyDemos();
+    try {
+        copyViewer();
+        copyMe();
+        copyMVSStories();
+        copyDemos();
+    } catch (e) {
+        console.error(e);
+    }
+}
+
+function copyToRepository() {
+    console.log('\n###', 'copy repository files');
+    fse.copySync(localPath, repositoryPath, { overwrite: true });
+}
+
+function syncRepository() {
+    console.log('\n###', 'sync repository');
+    if (!fs.existsSync(path.resolve(repositoryPath, '.git/'))) {
+        console.log('\n###', 'clone repository');
+        git()
+            .outputHandler(log)
+            .clone(remoteUrl, repositoryPath)
+            .fetch(['--all'])
+            .exec(copyToRepository);
+    } else {
+        console.log('\n###', 'update repository');
+        git()
+            .outputHandler(log)
+            .fetch(['--all'])
+            .reset(['--hard', 'origin/master'])
+            .exec(copyToRepository);
+    }
+}
+
+function commit() {
+    console.log('\n###', 'commit changes');
+    git()
+        .outputHandler(log)
+        .add(['-A'])
+        .commit(`Updated Apps and Demos
+- Mol* version: ${VERSION}
+- MVS Stories version: ${MVS_STORIES_VERSION}`)
+        .push();
 }
 
 if (!fs.existsSync(localPath)) {
@@ -62,26 +162,28 @@ if (!fs.existsSync(localPath)) {
     fs.mkdirSync(localPath, { recursive: true });
 }
 
-process.chdir(localPath);
+const argParser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Mol* Deploy'
+});
+argParser.add_argument('--local',{
+    help: 'Do not commit to remote repository.',
+    required: false,
+    action: 'store_true',
+});
+const args = argParser.parse_args();
 
-if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
-    console.log('\n###', 'clone repository');
-    git()
-        .outputHandler(log)
-        .clone(remoteUrl, localPath)
-        .fetch(['--all'])
-        .exec(copyFiles)
-        .add(['-A'])
-        .commit('updated viewer & demos')
-        .push();
-} else {
-    console.log('\n###', 'update repository');
-    git()
-        .outputHandler(log)
-        .fetch(['--all'])
-        .reset(['--hard', 'origin/master'])
-        .exec(copyFiles)
-        .add(['-A'])
-        .commit('updated viewer & demos')
-        .push();
-}
+copyFiles();
+
+if (args.local) {
+    process.exit(0);
+}
+
+if (!fs.existsSync(repositoryPath)) {
+    console.log('\n###', 'create repositoryPath');
+    fs.mkdirSync(repositoryPath, { recursive: true });
+}
+
+process.chdir(repositoryPath);
+syncRepository();
+commit();

scripts/write-version.mjs

@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as fs from 'fs';
+
+const VERSION = JSON.parse(fs.readFileSync('./package.json', 'utf8')).version;
+const TIMESTAMP = Date.now();
+const file = `export var PLUGIN_VERSION = '${VERSION}';\nexport var PLUGIN_VERSION_DATE = new Date(${TIMESTAMP})`;
+const files = ['./lib/mol-plugin/version.js', './lib/commonjs/mol-plugin/version.js'];
+for (const f of files) {
+    if (!fs.existsSync(f)) continue;
+    fs.writeFileSync(f, file);
+}

src/apps/docking-viewer/index.ts

@@ -9,6 +9,7 @@ import { Structure } from '../../mol-model/structure';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { PluginStateObject as PSO, PluginStateTransform } from '../../mol-plugin-state/objects';
 import { createPluginUI } from '../../mol-plugin-ui';
+import { renderReact18 } from '../../mol-plugin-ui/react18';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
 import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
@@ -26,7 +27,7 @@ import { ObjectKeys } from '../../mol-util/type-helpers';
 import './index.html';
 import { ShowButtons, StructurePreset, ViewportComponent } from './viewport';
 
-require('mol-plugin-ui/skin/light.scss');
+import '../../mol-plugin-ui/skin/light.scss';
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
@@ -58,20 +59,22 @@ class Viewer {
     }
 
     static async create(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
-        const o = { ...DefaultViewerOptions, ...{
-            layoutIsExpanded: false,
-            layoutShowControls: false,
-            layoutShowRemoteState: false,
-            layoutShowSequence: true,
-            layoutShowLog: false,
-            layoutShowLeftPanel: true,
+        const o = {
+            ...DefaultViewerOptions, ...{
+                layoutIsExpanded: false,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
 
-            viewportShowExpand: true,
-            viewportShowControls: false,
-            viewportShowSettings: false,
-            viewportShowSelectionMode: false,
-            viewportShowAnimation: false,
-        } };
+                viewportShowExpand: true,
+                viewportShowControls: false,
+                viewportShowSettings: false,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+            }
+        };
         const defaultSpec = DefaultPluginUISpec();
 
         const spec: PluginUISpec = {
@@ -126,7 +129,7 @@ class Viewer {
             ? document.getElementById(elementOrId)
             : elementOrId;
         if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
-        const plugin = await createPluginUI(element, spec);
+        const plugin = await createPluginUI({ target: element, spec, render: renderReact18 });
 
         (plugin.customState as any) = {
             colorPalette: {
@@ -135,18 +138,16 @@ class Viewer {
             }
         };
 
-        plugin.behaviors.canvas3d.initialized.subscribe(v => {
-            if (v) {
-                PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
-                    renderer: {
-                        ...plugin.canvas3d!.props.renderer,
-                        backgroundColor: ColorNames.white,
-                    },
-                    camera: {
-                        ...plugin.canvas3d!.props.camera,
-                        helper: { axes: { name: 'off', params: {} } }
-                    }
-                } });
+        PluginCommands.Canvas3D.SetSettings(plugin, {
+            settings: {
+                renderer: {
+                    ...plugin.canvas3d!.props.renderer,
+                    backgroundColor: ColorNames.white,
+                },
+                camera: {
+                    ...plugin.canvas3d!.props.camera,
+                    helper: { axes: { name: 'off', params: {} } }
+                }
             }
         });
 
@@ -166,7 +167,7 @@ class Viewer {
             structures.push({ ref: structureProperties?.ref || structure.ref });
         }
 
-        // remove current structuresfrom hierarchy as they will be merged
+        // remove current structures from hierarchy as they will be merged
         // TODO only works with using loadStructuresFromUrlsAndMerge once
         //      need some more API metho to work with the hierarchy
         this.plugin.managers.structure.hierarchy.updateCurrent(this.plugin.managers.structure.hierarchy.current.structures, 'remove');

src/apps/docking-viewer/viewport.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -31,7 +31,8 @@ function shinyStyle(plugin: PluginContext) {
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
             occlusion: { name: 'off', params: {} },
-            outline: { name: 'off', params: {} }
+            shadow: { name: 'off', params: {} },
+            outline: { name: 'off', params: {} },
         }
     } });
 }
@@ -43,17 +44,13 @@ function occlusionStyle(plugin: PluginContext) {
         },
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
-            occlusion: { name: 'on', params: {
-                samples: 64,
-                radius: 8,
-                bias: 1.0,
-                blurKernelSize: 13
-            } },
             outline: { name: 'on', params: {
                 scale: 1.0,
                 threshold: 0.33,
                 color: Color(0x0000),
-            } }
+                includeTransparent: true,
+            } },
+            shadow: { name: 'off', params: {} },
         }
     } });
 }
@@ -201,14 +198,14 @@ const InteractionsPreset = StructureRepresentationPresetProvider({
         const components = {
             ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
             surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
-            interactions: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandPlusSurroundings, `interactions`)
+            interactions: await presetStaticComponent(plugin, structureCell, 'ligand'),
         };
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
             ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.3 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
             ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.1, sizeAspectRatio: 1 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
-            interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams, material: CustomMaterial }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
+            interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams, material: CustomMaterial, includeParent: true, parentDisplay: 'between' }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
             label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, material: CustomMaterial, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
         };
 

src/apps/mesoscale-explorer/app.ts

@@ -0,0 +1,308 @@
+/**
+ * Copyright (c) 2022-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mp4Export } from '../../extensions/mp4-export';
+import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
+import { createPluginUI } from '../../mol-plugin-ui';
+import { renderReact18 } from '../../mol-plugin-ui/react18';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { PluginSpec } from '../../mol-plugin/spec';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
+import { Backgrounds } from '../../extensions/backgrounds';
+import { LeftPanel, RightPanel } from './ui/panels';
+import { Color } from '../../mol-util/color';
+import { SpacefillRepresentationProvider } from '../../mol-repr/structure/representation/spacefill';
+import { PluginBehaviors } from '../../mol-plugin/behavior';
+import { MesoFocusLoci } from './behavior/camera';
+import { GraphicsMode, MesoscaleState } from './data/state';
+import { MesoSelectLoci } from './behavior/select';
+import { Transparency } from '../../mol-gl/webgl/render-item';
+import { LoadModel, loadExampleEntry, loadPdb, loadPdbIhm, loadUrl, openState } from './ui/states';
+import { Asset } from '../../mol-util/assets';
+import { AnimateCameraSpin } from '../../mol-plugin-state/animation/built-in/camera-spin';
+import { AnimateCameraRock } from '../../mol-plugin-state/animation/built-in/camera-rock';
+import { AnimateStateSnapshots } from '../../mol-plugin-state/animation/built-in/state-snapshots';
+import { MesoViewportSnapshotDescription } from './ui/entities';
+
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setDebugMode, setProductionMode, setTimingMode, consoleStats } from '../../mol-util/debug';
+
+export type ExampleEntry = {
+    id: string,
+    label: string,
+    url: string,
+    type: 'molx' | 'molj' | 'cif' | 'bcif',
+    description?: string,
+    link?: string,
+}
+
+export type MesoscaleExplorerState = {
+    examples?: ExampleEntry[],
+    graphicsMode: GraphicsMode,
+    illumination: boolean,
+    stateRef?: string,
+    driver?: any,
+    stateCache: { [k: string]: any },
+}
+
+//
+
+const Extensions = {
+    'backgrounds': PluginSpec.Behavior(Backgrounds),
+    'mp4-export': PluginSpec.Behavior(Mp4Export),
+};
+
+const DefaultMesoscaleExplorerOptions = {
+    customFormats: [] as [string, DataFormatProvider][],
+    extensions: ObjectKeys(Extensions),
+    layoutIsExpanded: true,
+    layoutShowControls: true,
+    layoutShowRemoteState: true,
+    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
+    layoutShowSequence: true,
+    layoutShowLog: true,
+    layoutShowLeftPanel: true,
+    collapseLeftPanel: false,
+    collapseRightPanel: false,
+    disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
+    pixelScale: PluginConfig.General.PixelScale.defaultValue,
+    pickScale: PluginConfig.General.PickScale.defaultValue,
+    transparency: 'blended' as Transparency,
+    preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
+    allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
+    powerPreference: PluginConfig.General.PowerPreference.defaultValue,
+    resolutionMode: PluginConfig.General.ResolutionMode.defaultValue,
+    illumination: false,
+
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
+    viewportShowSelectionMode: true,
+    viewportShowAnimation: false,
+    viewportShowTrajectoryControls: false,
+    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
+    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
+    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
+    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+    saccharideCompIdMapType: 'default' as SaccharideCompIdMapType,
+
+    graphicsMode: 'quality' as GraphicsMode,
+    driver: undefined
+};
+type MesoscaleExplorerOptions = typeof DefaultMesoscaleExplorerOptions;
+
+export class MesoscaleExplorer {
+    constructor(public plugin: PluginUIContext) {
+    }
+
+    async loadExample(id: string) {
+        const entries = (this.plugin.customState as MesoscaleExplorerState).examples || [];
+        const entry = entries.find(e => e.id === id);
+        if (entry !== undefined) {
+            await loadExampleEntry(this.plugin, entry);
+        }
+    }
+
+    async loadUrl(url: string, type: 'molx' | 'molj' | 'cif' | 'bcif') {
+        await loadUrl(this.plugin, url, type);
+    }
+
+    async loadPdb(id: string) {
+        await loadPdb(this.plugin, id);
+    }
+
+    /**
+     * @deprecated Scheduled for removal in v5. Use {@link loadPdbIhm | loadPdbIhm(id: string)} instead.
+     */
+    async loadPdbDev(id: string) {
+        await this.loadPdbIhm(id);
+    }
+
+    async loadPdbIhm(id: string) {
+        await loadPdbIhm(this.plugin, id);
+    }
+
+    static async create(elementOrId: string | HTMLElement, options: Partial<MesoscaleExplorerOptions> = {}) {
+        const definedOptions = {} as any;
+        // filter for defined properies only so the default values
+        // are property applied
+        for (const p of Object.keys(options) as (keyof MesoscaleExplorerOptions)[]) {
+            if (options[p] !== void 0) definedOptions[p] = options[p];
+        }
+
+        const o: MesoscaleExplorerOptions = { ...DefaultMesoscaleExplorerOptions, ...definedOptions };
+        const defaultSpec = DefaultPluginUISpec();
+
+        const spec: PluginUISpec = {
+            actions: defaultSpec.actions,
+            behaviors: [
+                PluginSpec.Behavior(PluginBehaviors.Camera.CameraAxisHelper),
+                PluginSpec.Behavior(PluginBehaviors.Camera.CameraControls),
+                PluginSpec.Behavior(PluginBehaviors.State.SnapshotControls),
+
+                PluginSpec.Behavior(MesoFocusLoci),
+                PluginSpec.Behavior(MesoSelectLoci),
+                PluginSpec.Behavior(PluginBehaviors.Representation.SelectLoci),
+                ...o.extensions.map(e => Extensions[e]),
+            ],
+            animations: [
+                AnimateCameraSpin,
+                AnimateCameraRock,
+                AnimateStateSnapshots,
+            ],
+            customParamEditors: defaultSpec.customParamEditors,
+            customFormats: o?.customFormats,
+            layout: {
+                initial: {
+                    isExpanded: o.layoutIsExpanded,
+                    showControls: o.layoutShowControls,
+                    controlsDisplay: o.layoutControlsDisplay,
+                    regionState: {
+                        bottom: 'full',
+                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                        right: o.collapseRightPanel ? 'hidden' : 'full',
+                        top: 'full',
+                    }
+                },
+            },
+            components: {
+                ...defaultSpec.components,
+                controls: {
+                    ...defaultSpec.components?.controls,
+                    top: 'none',
+                    bottom: 'none',
+                    left: LeftPanel,
+                    right: RightPanel,
+                },
+                remoteState: 'none',
+                viewport: {
+                    snapshotDescription: MesoViewportSnapshotDescription,
+                }
+            },
+            config: [
+                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
+                [PluginConfig.General.PixelScale, o.pixelScale],
+                [PluginConfig.General.PickScale, o.pickScale],
+                [PluginConfig.General.Transparency, o.transparency],
+                [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
+                [PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
+                [PluginConfig.General.PowerPreference, o.powerPreference],
+                [PluginConfig.General.ResolutionMode, o.resolutionMode],
+                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
+                [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                [PluginConfig.Viewport.ShowTrajectoryControls, o.viewportShowTrajectoryControls],
+                [PluginConfig.State.DefaultServer, o.pluginStateServer],
+                [PluginConfig.State.CurrentServer, o.pluginStateServer],
+                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
+                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+                [PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
+            ]
+        };
+
+        const element = typeof elementOrId === 'string'
+            ? document.getElementById(elementOrId)
+            : elementOrId;
+        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
+
+        const plugin = await createPluginUI({
+            target: element,
+            spec,
+            render: renderReact18,
+            onBeforeUIRender: async plugin => {
+                let examples: MesoscaleExplorerState['examples'] = undefined;
+                try {
+                    examples = await plugin.fetch({ url: '../examples/list.json', type: 'json' }).run();
+                    // extend the array with file tour.json if it exists
+                    const tour = await plugin.fetch({ url: '../examples/tour.json', type: 'json' }).run();
+                    if (tour) {
+                        examples = examples?.concat(tour);
+                    }
+                } catch (e) {
+                    console.log(e);
+                }
+
+                (plugin.customState as MesoscaleExplorerState) = {
+                    examples,
+                    graphicsMode: o.graphicsMode,
+                    illumination: o.illumination,
+                    driver: o.driver,
+                    stateCache: {},
+                };
+
+                await MesoscaleState.init(plugin);
+            }
+        });
+
+        plugin.canvas3d?.setProps({
+            renderer: {
+                backgroundColor: Color(0x101010),
+            },
+            cameraFog: { name: 'off', params: {} },
+            hiZ: { enabled: true },
+            xr: {
+                disablePostprocessing: false,
+                sceneRadiusInMeters: 0.75,
+            },
+        });
+
+        plugin.representation.structure.registry.clear();
+        plugin.representation.structure.registry.add(SpacefillRepresentationProvider);
+
+        plugin.state.setSnapshotParams({
+            image: true,
+            componentManager: false,
+            structureSelection: true,
+        });
+
+        plugin.managers.lociLabels.clearProviders();
+
+        plugin.managers.dragAndDrop.addHandler('mesoscale-explorer', (files) => {
+            const sessions = files.filter(f => {
+                const fn = f.name.toLowerCase();
+                return fn.endsWith('.molx') || fn.endsWith('.molj');
+            });
+
+            if (sessions.length > 0) {
+                openState(plugin, sessions[0]);
+            } else {
+                plugin.runTask(plugin.state.data.applyAction(LoadModel, {
+                    files: files.map(f => Asset.File(f)),
+                }));
+            }
+
+            return true;
+        });
+
+        plugin.state.events.object.created.subscribe(e => {
+            (plugin.customState as MesoscaleExplorerState).stateCache = {};
+        });
+
+        plugin.state.events.object.removed.subscribe(e => {
+            (plugin.customState as MesoscaleExplorerState).stateCache = {};
+        });
+
+        return new MesoscaleExplorer(plugin);
+    }
+
+    handleResize() {
+        this.plugin.layout.events.updated.next(void 0);
+    }
+
+    dispose() {
+        this.plugin.dispose();
+    }
+}

src/apps/mesoscale-explorer/behavior/camera.ts

@@ -0,0 +1,99 @@
+/**
+ * Copyright (c) 2023-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Loci } from '../../../mol-model/loci';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../../../mol-plugin/behavior';
+import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observer';
+import { Binding } from '../../../mol-util/binding';
+import { PluginCommands } from '../../../mol-plugin/commands';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { StructureElement } from '../../../mol-model/structure';
+
+const B = ButtonsType;
+const M = ModifiersKeys;
+const Trigger = Binding.Trigger;
+const Key = Binding.TriggerKey;
+
+const DefaultMesoFocusLociBindings = {
+    clickCenter: Binding([
+        Trigger(B.Flag.Primary, M.create()),
+        Trigger(B.Flag.Trigger),
+    ], 'Camera center', 'Click element using ${triggers}'),
+    clickCenterFocus: Binding([
+        Trigger(B.Flag.Secondary, M.create()),
+    ], 'Camera center and focus', 'Click element using ${triggers}'),
+    keyCenterOnly: Binding([Key('C')], 'Center Only Toggle', 'Press ${triggers}'),
+};
+
+export const MesoFocusLociParams = {
+    minRadius: PD.Numeric(8, { min: 1, max: 50, step: 1 }),
+    extraRadius: PD.Numeric(4, { min: 1, max: 50, step: 1 }, { description: 'Value added to the bounding-sphere radius of the Loci' }),
+    durationMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'Camera transition duration' }),
+    centerOnly: PD.Boolean(true, { description: 'Keep current camera distance' }),
+    bindings: PD.Value(DefaultMesoFocusLociBindings, { isHidden: true }),
+};
+type MesoFocusLociProps = PD.Values<typeof MesoFocusLociParams>
+
+export const MesoFocusLoci = PluginBehavior.create<MesoFocusLociProps>({
+    name: 'camera-meso-focus-loci',
+    category: 'interaction',
+    ctor: class extends PluginBehavior.Handler<MesoFocusLociProps> {
+        register(): void {
+            this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
+                const { canvas3d } = this.ctx;
+                if (!canvas3d) return;
+
+                const loci = Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
+                const sphere = Loci.getBoundingSphere(loci) || Sphere3D();
+
+                const { clickCenter, clickCenterFocus } = this.params.bindings;
+                const { durationMs, extraRadius, minRadius, centerOnly } = this.params;
+                const radius = Math.max(sphere.radius + extraRadius, minRadius);
+
+                if (Binding.match(clickCenter, button, modifiers)) {
+                    // left mouse button
+                    if (Loci.isEmpty(current.loci)) {
+                        PluginCommands.Camera.Reset(this.ctx, { });
+                        return;
+                    }
+                    if (StructureElement.Loci.is(current.loci)) {
+                        if (centerOnly) {
+                            const snapshot = canvas3d.camera.getCenter(sphere.center);
+                            canvas3d.requestCameraReset({ durationMs, snapshot });
+                        } else {
+                            this.ctx.managers.camera.focusSphere(sphere, this.params);
+                        }
+                    }
+                } else if (Binding.match(clickCenterFocus, button, modifiers)) {
+                    // right mouse button
+                    if (Loci.isEmpty(current.loci)) {
+                        PluginCommands.Camera.Reset(this.ctx, { });
+                        return;
+                    }
+                    if (centerOnly) {
+                        const snapshot = canvas3d.camera.getCenter(sphere.center, radius);
+                        canvas3d.requestCameraReset({ durationMs, snapshot });
+                    } else {
+                        this.ctx.managers.camera.focusSphere(sphere, this.params);
+                    }
+                }
+            });
+
+            this.subscribeObservable(this.ctx.behaviors.interaction.key, ({ code, key, modifiers }) => {
+                if (!this.ctx.canvas3d) return;
+                const b = { ...DefaultMesoFocusLociBindings, ...this.params.bindings };
+                const { centerOnly } = this.params;
+
+                if (Binding.matchKey(b.keyCenterOnly, code, modifiers, key)) {
+                    this.params.centerOnly = !centerOnly;
+                }
+            });
+        }
+    },
+    params: () => MesoFocusLociParams,
+    display: { name: 'Camera Meso Focus Loci on Canvas' }
+});

src/apps/mesoscale-explorer/behavior/select.ts

@@ -0,0 +1,209 @@
+/**
+ * Copyright (c) 2023-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { EveryLoci, Loci } from '../../../mol-model/loci';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../../../mol-plugin/behavior';
+import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observer';
+import { Binding } from '../../../mol-util/binding';
+import { PluginStateObject as SO } from '../../../mol-plugin-state/objects';
+import { Structure, StructureElement } from '../../../mol-model/structure';
+import { StateSelection } from '../../../mol-state';
+import { StateTreeSpine } from '../../../mol-state/tree/spine';
+import { Representation } from '../../../mol-repr/representation';
+import { MarkerAction } from '../../../mol-util/marker-action';
+import { PluginContext } from '../../../mol-plugin/context';
+import { MesoscaleState, expandAllGroups, getCellDescription, getEveryEntity } from '../data/state';
+
+const B = ButtonsType;
+const M = ModifiersKeys;
+const Trigger = Binding.Trigger;
+
+const DefaultMesoSelectLociBindings = {
+    click: Binding([
+        Trigger(B.Flag.Primary, M.create()),
+        Trigger(B.Flag.Trigger),
+    ], 'Click', 'Click element using ${triggers}'),
+    clickToggleSelect: Binding([
+        Trigger(B.Flag.Primary, M.create({ shift: true })),
+        Trigger(B.Flag.Primary, M.create({ control: true })),
+    ], 'Toggle select', 'Click element using ${triggers}'),
+    hoverHighlightOnly: Binding([
+        Trigger(B.Flag.None, M.create({ shift: true })),
+        Trigger(B.Flag.None, M.create({ control: true })),
+    ], 'Highlight', 'Hover element using ${triggers}'),
+};
+const MesoSelectLociParams = {
+    bindings: PD.Value(DefaultMesoSelectLociBindings, { isHidden: true }),
+};
+type MesoSelectLociProps = PD.Values<typeof MesoSelectLociParams>
+
+export const MesoSelectLoci = PluginBehavior.create<MesoSelectLociProps>({
+    name: 'camera-meso-select-loci',
+    category: 'interaction',
+    ctor: class extends PluginBehavior.Handler<MesoSelectLociProps> {
+        private spine: StateTreeSpine.Impl;
+        private lociMarkProvider = (interactionLoci: Representation.Loci, action: MarkerAction) => {
+            if (!this.ctx.canvas3d) return;
+            this.ctx.canvas3d.mark(interactionLoci, action);
+        };
+        private applySelectMark(ref: string, clear?: boolean) {
+            const cell = this.ctx.state.data.cells.get(ref);
+            if (cell && SO.isRepresentation3D(cell.obj)) {
+                this.spine.current = cell;
+                const so = this.spine.getRootOfType(SO.Molecule.Structure);
+                if (so) {
+                    if (clear) {
+                        this.lociMarkProvider({ loci: Structure.Loci(so.data) }, MarkerAction.Deselect);
+                    }
+                    const loci = this.ctx.managers.structure.selection.getLoci(so.data);
+                    this.lociMarkProvider({ loci }, MarkerAction.Select);
+                }
+            }
+        }
+        register(): void {
+            this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
+                if (!this.ctx.canvas3d || this.ctx.isBusy) return;
+
+                const { click, clickToggleSelect } = this.params.bindings;
+                if (Binding.match(clickToggleSelect, button, modifiers)) {
+                    if (Loci.isEmpty(current.loci)) {
+                        this.ctx.managers.interactivity.lociSelects.deselectAll();
+                        return;
+                    }
+                    const loci = Loci.normalize(current.loci, modifiers.control ? 'entity' : this.ctx.managers.interactivity.props.granularity);
+                    this.ctx.managers.interactivity.lociSelects.toggle({ loci }, false);
+                    if (StructureElement.Loci.is(current.loci)) {
+                        const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
+                        const d = getCellDescription(cell!);
+                        MesoscaleState.set(this.ctx, { focusInfo: `${d}` });
+                    }
+                }
+                if (Binding.match(click, button, modifiers)) {
+                    if (Loci.isEmpty(current.loci)) {
+                        MesoscaleState.set(this.ctx, { focusInfo: '', filter: '' });
+                        return;
+                    }
+                    const snapshotKey = current.repr?.props?.snapshotKey?.trim() ?? '';
+                    if (snapshotKey) {
+                        this.ctx.managers.snapshot.applyKey(snapshotKey);
+                    } else {
+                        if (StructureElement.Loci.is(current.loci)) {
+                            const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
+                            const d = getCellDescription(cell!);
+                            MesoscaleState.set(this.ctx, { focusInfo: `${d}`, filter: `${cell?.obj?.label}` });
+                            expandAllGroups(this.ctx);
+                        }
+                    }
+                }
+            });
+            this.ctx.managers.interactivity.lociSelects.addProvider(this.lociMarkProvider);
+
+            this.subscribeObservable(this.ctx.behaviors.interaction.hover, ({ current, button, modifiers }) => {
+                if (!this.ctx.canvas3d || this.ctx.isBusy) return;
+
+                const pointerLock = !!this.ctx.canvas3dContext?.input.pointerLock;
+                const { hoverHighlightOnly } = this.params.bindings;
+
+                if (!pointerLock && Binding.match(hoverHighlightOnly, button, modifiers)) {
+                    if (Loci.isEmpty(current.loci)) {
+                        this.ctx.managers.interactivity.lociHighlights.clearHighlights();
+                        return;
+                    }
+                    if (StructureElement.Loci.is(current.loci)) {
+                        if (modifiers.control) {
+                            this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EveryLoci }, false);
+                        } else {
+                            const loci = Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
+                            this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci }, false);
+                        }
+                    }
+                }
+
+                if (Loci.isEmpty(current.loci)) {
+                    this.ctx.behaviors.labels.highlight.next({ labels: [] });
+                    this.ctx.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+                } else {
+                    const labels: string[] = [];
+                    if (StructureElement.Loci.is(current.loci)) {
+                        const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
+                        const d = getCellDescription(cell!);
+                        labels.push(d);
+                    } else {
+                        const loci = Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
+                        if (loci.kind === 'group-loci') {
+                            if ('shape' in current.loci && current.loci.shape.geometry.kind === 'text') {
+                                const qname = current.repr?.props.customText;
+                                // highlight protein with same name
+                                const entities = getEveryEntity(this.ctx, qname);
+                                for (const r of entities) {
+                                    const repr = r.obj?.data.repr;
+                                    if (repr) {
+                                        this.ctx.canvas3d?.mark({ repr, loci: EveryLoci }, MarkerAction.Highlight);
+                                    }
+                                }
+                            }
+                            labels.push(loci.shape.getLabel(0, 0));
+                        }
+                    }
+                    this.ctx.behaviors.labels.highlight.next({ labels });
+                }
+            });
+            this.ctx.managers.interactivity.lociHighlights.addProvider(this.lociMarkProvider);
+
+            let dimDisabled = false;
+
+            this.subscribeObservable(this.ctx.behaviors.interaction.keyReleased, ({ code, modifiers }) => {
+                if (!this.ctx.canvas3d) return;
+
+                if ((code.startsWith('Shift') && !modifiers.control) || (code.startsWith('Control') && !modifiers.shift)) {
+                    if (dimDisabled) {
+                        dimDisabled = false;
+                        this.ctx.canvas3d?.setProps({ renderer: { dimStrength: 1 } }, true);
+                    }
+                    this.ctx.managers.interactivity.lociHighlights.clearHighlights();
+                }
+            });
+
+            this.subscribeObservable(this.ctx.behaviors.interaction.key, ({ modifiers }) => {
+                if (!this.ctx.canvas3d) return;
+
+                if (!dimDisabled && modifiers.control && modifiers.shift) {
+                    dimDisabled = true;
+                    this.ctx.canvas3d?.setProps({ renderer: { dimStrength: 0 } });
+                }
+            });
+
+            this.subscribeObservable(this.ctx.state.events.object.created, ({ ref }) => this.applySelectMark(ref));
+
+            // re-apply select-mark to all representation of an updated structure
+            this.subscribeObservable(this.ctx.state.events.object.updated, ({ ref, obj, oldObj, oldData, action }) => {
+                const cell = this.ctx.state.data.cells.get(ref);
+                if (cell && SO.Molecule.Structure.is(cell.obj)) {
+                    const structure: Structure = obj.data;
+                    const oldStructure: Structure | undefined = action === 'recreate' ? oldObj?.data :
+                        action === 'in-place' ? oldData : undefined;
+                    if (oldStructure &&
+                        Structure.areEquivalent(structure, oldStructure) &&
+                        Structure.areHierarchiesEqual(structure, oldStructure)) return;
+
+                    const reprs = this.ctx.state.data.select(StateSelection.children(ref).ofType(SO.Molecule.Structure.Representation3D));
+                    for (const repr of reprs) this.applySelectMark(repr.transform.ref, true);
+                }
+            });
+        }
+        unregister() {
+            this.ctx.managers.interactivity.lociSelects.removeProvider(this.lociMarkProvider);
+            this.ctx.managers.interactivity.lociHighlights.removeProvider(this.lociMarkProvider);
+        }
+        constructor(ctx: PluginContext, params: MesoSelectLociProps) {
+            super(ctx, params);
+            this.spine = new StateTreeSpine.Impl(ctx.state.data.cells);
+        }
+    },
+    params: () => MesoSelectLociParams,
+    display: { name: 'Camera Meso Select Loci on Canvas' }
+});

src/apps/mesoscale-explorer/data/cellpack/model.ts

@@ -0,0 +1,175 @@
+/**
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { SortedArray } from '../../../../mol-data/int';
+import { SymmetryOperator } from '../../../../mol-math/geometry';
+import { Mat4 } from '../../../../mol-math/linear-algebra';
+import { ModelSymmetry } from '../../../../mol-model-formats/structure/property/symmetry';
+import { CustomStructureProperty } from '../../../../mol-model-props/common/custom-structure-property';
+import { ElementIndex, EntityIndex, Model, Structure, Unit } from '../../../../mol-model/structure';
+import { Assembly, Symmetry } from '../../../../mol-model/structure/model/properties/symmetry';
+import { PluginStateObject as PSO, PluginStateTransform } from '../../../../mol-plugin-state/objects';
+import { PluginContext } from '../../../../mol-plugin/context';
+import { Task } from '../../../../mol-task';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+
+function createModelChainMap(model: Model) {
+    const builder = new Structure.StructureBuilder();
+    const units = new Map<string, Unit>();
+
+    const { label_asym_id, _rowCount } = model.atomicHierarchy.chains;
+    const { offsets } = model.atomicHierarchy.chainAtomSegments;
+
+    for (let i = 0; i < _rowCount; i++) {
+        const elements = SortedArray.ofBounds(offsets[i] as ElementIndex, offsets[i + 1] as ElementIndex);
+        const unit = builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements, Unit.Trait.FastBoundary);
+        units.set(label_asym_id.value(i), unit);
+    }
+
+    return units;
+}
+
+function buildCellpackAssembly(model: Model, assembly: Assembly) {
+    const coordinateSystem = SymmetryOperator.create(assembly.id, Mat4.identity(), { assembly: { id: assembly.id, operId: 0, operList: [] } });
+    const assembler = Structure.Builder({
+        coordinateSystem,
+        label: model.label,
+    });
+
+    const units = createModelChainMap(model);
+
+    for (const g of assembly.operatorGroups) {
+        for (const oper of g.operators) {
+            for (const id of g.asymIds!) {
+                const u = units.get(id);
+                if (u) {
+                    assembler.addWithOperator(u, oper);
+                } else {
+                    console.log(`missing asymId '${id}'`);
+                }
+            }
+        }
+    }
+
+    return assembler.getStructure();
+}
+
+export { CellpackAssembly };
+type CellpackAssembly = typeof CellpackAssembly
+const CellpackAssembly = PluginStateTransform.BuiltIn({
+    name: 'cellpack-assembly',
+    display: { name: 'Cellpack Assembly' },
+    from: PSO.Molecule.Model,
+    to: PSO.Molecule.Structure,
+    params: {
+        id: PD.Text('', { label: 'Asm Id', description: 'Assembly Id (use empty for the 1st assembly)' }),
+    }
+})({
+    canAutoUpdate({ newParams }) {
+        return true;
+    },
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Build Structure', async ctx => {
+            const model = a.data;
+
+            let id = params.id;
+            let asm: Assembly | undefined = void 0;
+            const symmetry = ModelSymmetry.Provider.get(model);
+
+            // if no id is specified, use the 1st assembly.
+            if (!id && symmetry && symmetry.assemblies.length !== 0) {
+                id = symmetry.assemblies[0].id;
+            }
+
+            if (!symmetry || symmetry.assemblies.length === 0) {
+                plugin.log.warn(`Model '${model.entryId}' has no assembly, returning model structure.`);
+            } else {
+                asm = Symmetry.findAssembly(model, id || '');
+                if (!asm) {
+                    plugin.log.warn(`Model '${model.entryId}' has no assembly called '${id}', returning model structure.`);
+                }
+            }
+
+            const base = Structure.ofModel(model);
+            if (!asm) {
+                const label = { label: 'Model', description: Structure.elementDescription(base) };
+                return new PSO.Molecule.Structure(base, label);
+            }
+
+            const s = buildCellpackAssembly(model, asm);
+
+            const objProps = { label: `Assembly ${id}`, description: Structure.elementDescription(s) };
+            return new PSO.Molecule.Structure(s, objProps);
+        });
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});
+
+type UnitsByEntity = Map<EntityIndex, Unit[]>;
+const UnitsByEntity = CustomStructureProperty.createSimple<UnitsByEntity>('units_by_entity', 'root');
+
+function getUnitsByEntity(structure: Structure): UnitsByEntity {
+    if (UnitsByEntity.get(structure).value) {
+        return UnitsByEntity.get(structure).value!;
+    }
+
+    const atomicIndex = structure.model.atomicHierarchy.index;
+    const map: UnitsByEntity = new Map();
+    for (const ug of structure.unitSymmetryGroups) {
+        const u = ug.units[0] as Unit.Atomic;
+        const e = atomicIndex.getEntityFromChain(u.chainIndex[u.elements[0]]);
+
+        if (!map.has(e)) map.set(e, []);
+        const entityUnits = map.get(e)!;
+
+        for (let i = 0, il = ug.units.length; i < il; ++i) {
+            entityUnits.push(ug.units[i]);
+        }
+    }
+
+    UnitsByEntity.set(structure, { value: map }, map);
+    return map;
+}
+
+export { CellpackStructure };
+type CellpackStructure = typeof CellpackStructure
+const CellpackStructure = PluginStateTransform.BuiltIn({
+    name: 'cellpack-structure',
+    display: { name: 'Cellpack Structure' },
+    from: PSO.Root,
+    to: PSO.Molecule.Structure,
+    params: {
+        structureRef: PD.Text(''),
+        entityId: PD.Text('')
+    }
+})({
+    canAutoUpdate({ newParams }) {
+        return true;
+    },
+    apply({ a, params, dependencies }) {
+        return Task.create('Build Structure', async ctx => {
+            const parent = dependencies![params.structureRef].data as Structure;
+            const { entities } = parent.model;
+            const idx = entities.getEntityIndex(params.entityId);
+
+            const unitsByEntity = getUnitsByEntity(parent);
+            const units = unitsByEntity.get(idx) || [];
+
+            const structure = Structure.create(units);
+            const description_label = entities.data.pdbx_description.value(idx)[0] || 'model';
+            const label = description_label.split('.').at(-1) || a.label;
+            const description = entities.data.pdbx_parent_entity_id.value(idx) || label;
+            return new PSO.Molecule.Structure(structure, { label, description: description }); // `${a.description}`
+        });
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});

src/apps/mesoscale-explorer/data/cellpack/preset.ts

@@ -0,0 +1,233 @@
+/**
+ * Copyright (c) 2019-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ */
+
+import { PluginStateObject } from '../../../../mol-plugin-state/objects';
+import { StructureRepresentation3D } from '../../../../mol-plugin-state/transforms/representation';
+import { PluginContext } from '../../../../mol-plugin/context';
+import { SpacefillRepresentationProvider } from '../../../../mol-repr/structure/representation/spacefill';
+import { StateObjectRef, StateObjectSelector, StateBuilder } from '../../../../mol-state';
+import { Color } from '../../../../mol-util/color';
+import { ColorNames } from '../../../../mol-util/color/names';
+import { GraphicsMode, MesoscaleGroup, MesoscaleState, getDistinctBaseColors, getDistinctGroupColors, getGraphicsModeProps, getMesoscaleGroupParams } from '../state';
+import { CellpackAssembly, CellpackStructure } from './model';
+
+function getSpacefillParams(color: Color, sizeFactor: number, graphics: GraphicsMode, merge?: boolean) {
+    const gmp = getGraphicsModeProps(graphics === 'custom' ? 'quality' : graphics);
+    return {
+        type: {
+            name: 'spacefill',
+            params: {
+                ...SpacefillRepresentationProvider.defaultValues,
+                ignoreHydrogens: false,
+                instanceGranularity: true,
+                ignoreLight: true,
+                lodLevels: gmp.lodLevels,
+                quality: 'lowest', // avoid 'auto', triggers boundary calc
+                sizeFactor,
+                clip: {
+                    variant: merge ? 'pixel' : 'instance',
+                    objects: [],
+                },
+                clipPrimitive: true,
+                approximate: gmp.approximate,
+                alphaThickness: gmp.alphaThickness,
+                visuals: [merge ? 'structure-element-sphere' : 'element-sphere'],
+                interior: {
+                    color: Color.fromNormalizedRgb(0, 0, 0),
+                    colorStrength: 0.15,
+                    substance: { metalness: 0.0, roughness: 1.0, bumpiness: 0.0 },
+                    substanceStrength: 1,
+                }
+            },
+        },
+        colorTheme: {
+            name: 'uniform',
+            params: {
+                value: color,
+                saturation: 0,
+                lightness: 0,
+            }
+        },
+        sizeTheme: {
+            name: 'physical',
+            params: {
+                scale: 1,
+            }
+        },
+    };
+}
+
+function getSizeFactor(name: string): number {
+    switch (name) {
+        case 'dLDL':
+            return 2.5;
+        case 'iLDL':
+            return 5;
+        case 'NP_CA':
+        case 'POL_CA':
+        case 'FactorH1':
+        case 'iIgM_Antibody_5mer':
+        // case 'MG_271_272_273_274_192MER': // has a coarse and an atomic part
+            return 2;
+        default: return 1;
+    }
+}
+
+export async function createCellpackHierarchy(plugin: PluginContext, trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>) {
+    const builder = plugin.builders.structure;
+    const state = plugin.state.data;
+
+    const model = await builder.createModel(trajectory, { modelIndex: 0 });
+    const entities = model.data!.entities.data;
+
+    const compGroups = new Map<string, StateObjectSelector>();
+    const compIds = new Map<string, { idx: number, members: Map<string, number> }>();
+    const compColors = new Map<string, Color[]>();
+
+    const funcGroups = new Map<string, StateObjectSelector>();
+    const funcIds = new Map<string, { idx: number, size: number }>();
+    const funcColors = new Map<string, Color[]>();
+
+    const graphicsMode = MesoscaleState.get(plugin).graphics;
+    const groupParams = getMesoscaleGroupParams(graphicsMode);
+
+    const base = await state.build()
+        .to(model)
+        .apply(CellpackAssembly, { id: '' })
+        .commit();
+
+    const compRoot = await state.build()
+        .toRoot()
+        .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: 'comp:', label: 'compartment', color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .commit();
+
+    const funcRoot = await state.build()
+        .toRoot()
+        .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: 'func:', label: 'function', color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .commit();
+
+    if (entities._rowCount > 1) {
+        for (let i = 0; i < entities._rowCount; i++) {
+            const description = entities.pdbx_description.value(i)[0] || 'unknown compartment';
+            const d = description.split('.');
+            const n = d.slice(0, -1).join('.');
+            const l = d.at(-1)!;
+            if (!compIds.has(n)) {
+                compIds.set(n, { idx: compIds.size, members: new Map() });
+            }
+            const cm = compIds.get(n)!;
+            cm.members.set(l, cm.members.size);
+
+            const f = entities.details.value(i) || 'unknown function';
+            if (!funcIds.has(f)) {
+                funcIds.set(f, { idx: funcIds.size, size: 0 });
+            }
+            funcIds.get(f)!.size += 1;
+        }
+
+        //
+
+        const baseCompColors = getDistinctBaseColors(compIds.size, 0);
+        const compIdEntries = Array.from(compIds.entries());
+        for (let i = 0; i < compIdEntries.length; ++i) {
+            const [n, m] = compIdEntries[i];
+            const groupColors = getDistinctGroupColors(m.members.size, baseCompColors[i], 20, 0);
+            compColors.set(n, groupColors);
+        }
+
+        //
+
+        const baseFuncColors = getDistinctBaseColors(funcIds.size, 0);
+        const funcIdEntries = Array.from(funcIds.entries());
+        for (let i = 0; i < funcIdEntries.length; ++i) {
+            const [n, m] = funcIdEntries[i];
+            const groupColors = getDistinctGroupColors(m.size, baseFuncColors[i], 20, 0);
+            funcColors.set(n, groupColors);
+        }
+
+        //
+
+        for (let i = 0; i < entities._rowCount; i++) {
+            const description = entities.pdbx_description.value(i)[0] || 'unknown compartment';
+            const nodes = description.split('.');
+            for (let j = 0, jl = nodes.length - 1; j < jl; ++j) {
+                const n = nodes.slice(0, j + 1).join('.');
+                const p = nodes.slice(0, j).join('.');
+                if (!compGroups.has(n)) {
+                    const colorIdx = compIds.get(n)?.idx;
+                    const color = colorIdx !== undefined ? baseCompColors[colorIdx] : ColorNames.white;
+                    const label = nodes[j];
+                    const parent = compGroups.get(p) ?? compRoot;
+                    parent.cell!.state.isCollapsed = false;
+                    const group = await state.build()
+                        .to(parent)
+                        .apply(MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:comp:${n}`, `comp:${p}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                        .commit({ revertOnError: true });
+                    compGroups.set(n, group);
+                }
+            }
+
+            const f = entities.details.value(i) || 'unknown function';
+            if (!funcGroups.has(f)) {
+                const colorIdx = funcIds.get(f)?.idx;
+                const color = colorIdx !== undefined ? baseFuncColors[colorIdx] : ColorNames.white;
+                const group = await state.build()
+                    .to(funcRoot)
+                    .apply(MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:func:${f}`, 'func:'], state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                    .commit({ revertOnError: true });
+                funcGroups.set(f, group);
+            }
+        }
+
+        //
+
+        await state.transaction(async () => {
+            try {
+                const dependsOn = [base.ref];
+                plugin.animationLoop.stop({ noDraw: true });
+                let build: StateBuilder.Root | StateBuilder.To<any> = state.build();
+                for (let i = 0; i < entities._rowCount; i++) {
+                    const description = entities.pdbx_description.value(i)[0] || 'model';
+                    const d = description.split('.');
+                    const n = d.slice(0, -1).join('.');
+                    const l = d.at(-1)!;
+
+                    const f = entities.details.value(i) || 'unknown function';
+
+                    const color = compColors.get(n)![compIds.get(n)!.members.get(l)!];
+                    const sizeFactor = getSizeFactor(l);
+
+                    build = build
+                        .toRoot()
+                        .apply(CellpackStructure, { structureRef: base.ref, entityId: entities.id.value(i) }, { dependsOn })
+                        .apply(StructureRepresentation3D, getSpacefillParams(color, sizeFactor, graphicsMode), { tags: [`comp:${n}`, `func:${f}`] });
+                }
+                await build.commit();
+            } catch (e) {
+                console.error(e);
+                plugin.log.error(e);
+            } finally {
+                plugin.animationLoop.start();
+            }
+        }).run();
+    } else {
+        const dependsOn = [base.ref];
+
+        const merge = (
+            base.data &&
+            base.data.model.entities.data._rowCount === 1 &&
+            base.data.unitSymmetryGroups.length > 100 &&
+            base.data.unitSymmetryGroups.some(usg => usg.units.length > 1)
+        );
+
+        await state.build()
+            .toRoot()
+            .apply(CellpackStructure, { structureRef: base.ref, entityId: entities.id.value(0) }, { dependsOn })
+            .apply(StructureRepresentation3D, getSpacefillParams(ColorNames.lightgray, 1, graphicsMode, merge), { tags: [`comp:`, `func:`] })
+            .commit();
+    }
+}

src/apps/mesoscale-explorer/data/generic/model.ts

@@ -0,0 +1,140 @@
+/**
+ * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mat4 } from '../../../../mol-math/linear-algebra/3d/mat4';
+import { ElementIndex, Model, Structure, Unit } from '../../../../mol-model/structure';
+import { PluginStateObject as SO, PluginStateTransform } from '../../../../mol-plugin-state/objects';
+import { Task } from '../../../../mol-task';
+import { StateObject, StateTransformer } from '../../../../mol-state';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { SymmetryOperator } from '../../../../mol-math/geometry';
+import { mergeUnits, partitionUnits } from '../util';
+import { Assembly, Symmetry } from '../../../../mol-model/structure/model/properties/symmetry';
+import { ModelSymmetry } from '../../../../mol-model-formats/structure/property/symmetry';
+import { SortedArray } from '../../../../mol-data/int';
+import { GenericInstances, getTransforms } from './preset';
+import { Asset } from '../../../../mol-util/assets';
+import { PluginContext } from '../../../../mol-plugin/context';
+import { deepEqual } from '../../../../mol-util';
+
+function createModelChainMap(model: Model) {
+    const builder = new Structure.StructureBuilder();
+    const units = new Map<string, Unit>();
+
+    const { label_asym_id, _rowCount } = model.atomicHierarchy.chains;
+    const { offsets } = model.atomicHierarchy.chainAtomSegments;
+
+    for (let i = 0; i < _rowCount; i++) {
+        const elements = SortedArray.ofBounds(offsets[i] as ElementIndex, offsets[i + 1] as ElementIndex);
+        const unit = builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements, Unit.Trait.FastBoundary);
+        units.set(label_asym_id.value(i), unit);
+    }
+
+    return units;
+}
+
+function buildAssembly(model: Model, assembly: Assembly) {
+    const coordinateSystem = SymmetryOperator.create(assembly.id, Mat4.identity(), { assembly: { id: assembly.id, operId: 0, operList: [] } });
+    const assembler = Structure.Builder({
+        coordinateSystem,
+        label: model.label,
+    });
+
+    const units = createModelChainMap(model);
+
+    for (const g of assembly.operatorGroups) {
+        for (const oper of g.operators) {
+            for (const id of g.asymIds!) {
+                const u = units.get(id);
+                if (u) {
+                    assembler.addWithOperator(u, oper);
+                } else {
+                    console.log(`missing asymId '${id}'`);
+                }
+            }
+        }
+    }
+
+    return assembler.getStructure();
+}
+
+const EmptyInstances: GenericInstances<Asset> = {
+    positions: { data: [] },
+    rotations: { variant: 'euler', data: [] }
+};
+
+export { StructureFromGeneric };
+type StructureFromGeneric = typeof StructureFromGeneric
+const StructureFromGeneric = PluginStateTransform.BuiltIn({
+    name: 'structure-from-generic',
+    display: { name: 'Structure from Generic', description: 'Create a molecular structure from Generic models.' },
+    from: SO.Molecule.Model,
+    to: SO.Molecule.Structure,
+    params: {
+        instances: PD.Value<GenericInstances<Asset>>(EmptyInstances),
+        label: PD.Optional(PD.Text('')),
+        description: PD.Optional(PD.Text('')),
+        cellSize: PD.Numeric(500, { min: 0, max: 10000, step: 100 }),
+    }
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Build Structure', async ctx => {
+            const transforms = await getTransforms(plugin, params.instances);
+            if (transforms.length === 0) return StateObject.Null;
+
+            const model = a.data;
+            const label = params.label || model.label;
+
+            const base = Structure.ofModel(a.data);
+
+            let structure: Structure;
+            if (transforms.length === 1 && Mat4.isIdentity(transforms[0])) {
+                const symmetry = ModelSymmetry.Provider.get(model);
+                const id = symmetry?.assemblies[0]?.id;
+                const asm = Symmetry.findAssembly(model, id || '');
+                if (asm) {
+                    structure = buildAssembly(model, asm);
+                } else {
+                    const mergedUnits = partitionUnits(base.units, params.cellSize);
+                    structure = Structure.create(mergedUnits, { label });
+                }
+            } else {
+                const assembler = Structure.Builder({ label });
+                const unit = mergeUnits(base.units, 0);
+                for (let i = 0, il = transforms.length; i < il; ++i) {
+                    const t = transforms[i];
+                    const op = SymmetryOperator.create(`op-${i}`, t);
+                    assembler.addWithOperator(unit, op);
+                }
+                structure = assembler.getStructure();
+            }
+
+            const props = { label, description: params.description || Structure.elementDescription(structure) };
+            return new SO.Molecule.Structure(structure, props);
+        });
+    },
+    update({ newParams, oldParams }, plugin: PluginContext) {
+        if (deepEqual(newParams, oldParams)) {
+            return StateTransformer.UpdateResult.Unchanged;
+        }
+
+        if (oldParams.instances) releaseInstances(plugin, oldParams.instances);
+        return StateTransformer.UpdateResult.Recreate;
+    },
+    dispose({ b, params }, plugin: PluginContext) {
+        b?.data.customPropertyDescriptors.dispose();
+        if (params?.instances) releaseInstances(plugin, params.instances);
+    }
+});
+
+function releaseInstances(plugin: PluginContext, instances: GenericInstances<Asset>) {
+    if (!Array.isArray(instances.positions.data)) {
+        plugin.managers.asset.release(instances.positions.data.file);
+    }
+    if (!Array.isArray(instances.rotations.data)) {
+        plugin.managers.asset.release(instances.rotations.data.file);
+    }
+}

src/apps/mesoscale-explorer/data/generic/preset.ts

@@ -0,0 +1,586 @@
+/**
+ * Copyright (c) 2023-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mat4 } from '../../../../mol-math/linear-algebra/3d/mat4';
+import { StateBuilder, StateObjectSelector } from '../../../../mol-state';
+import { PluginContext } from '../../../../mol-plugin/context';
+import { SpacefillRepresentationProvider } from '../../../../mol-repr/structure/representation/spacefill';
+import { Color } from '../../../../mol-util/color';
+import { utf8Read } from '../../../../mol-io/common/utf8';
+import { Mat3, Quat, Vec3 } from '../../../../mol-math/linear-algebra';
+import { GraphicsMode, MesoscaleGroup, MesoscaleState, getGraphicsModeProps, getMesoscaleGroupParams } from '../state';
+import { ColorNames } from '../../../../mol-util/color/names';
+import { ShapeRepresentation3D, StructureRepresentation3D } from '../../../../mol-plugin-state/transforms/representation';
+import { ParseCif, ParsePly, ReadFile } from '../../../../mol-plugin-state/transforms/data';
+import { ModelFromTrajectory, ShapeFromPly, TrajectoryFromGRO, TrajectoryFromMOL, TrajectoryFromMOL2, TrajectoryFromMmCif, TrajectoryFromPDB, TrajectoryFromSDF, TrajectoryFromXYZ } from '../../../../mol-plugin-state/transforms/model';
+import { Euler } from '../../../../mol-math/linear-algebra/3d/euler';
+import { Asset } from '../../../../mol-util/assets';
+import { Clip } from '../../../../mol-util/clip';
+import { StructureFromGeneric } from './model';
+import { getFileNameInfo } from '../../../../mol-util/file-info';
+import { NumberArray } from '../../../../mol-util/type-helpers';
+import { BaseGeometry } from '../../../../mol-geo/geometry/base';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+
+function getSpacefillParams(color: Color, sizeFactor: number, graphics: GraphicsMode, clipVariant: Clip.Variant) {
+    const gmp = getGraphicsModeProps(graphics === 'custom' ? 'quality' : graphics);
+    return {
+        type: {
+            name: 'spacefill',
+            params: {
+                ...SpacefillRepresentationProvider.defaultValues,
+                ignoreHydrogens: true,
+                instanceGranularity: true,
+                ignoreLight: true,
+                lodLevels: gmp.lodLevels.map(l => {
+                    return {
+                        ...l,
+                        stride: Math.max(1, Math.round(l.stride / Math.pow(sizeFactor, l.scaleBias)))
+                    };
+                }),
+                quality: 'lowest', // avoid 'auto', triggers boundary calc
+                sizeFactor,
+                clip: {
+                    variant: clipVariant,
+                    objects: [],
+                },
+                clipPrimitive: true,
+                approximate: gmp.approximate,
+                alphaThickness: gmp.alphaThickness,
+                interior: {
+                    color: Color.fromNormalizedRgb(0, 0, 0),
+                    colorStrength: 0.15,
+                    substance: { metalness: 0.0, roughness: 1.0, bumpiness: 0.0 },
+                    substanceStrength: 1,
+                }
+            },
+        },
+        colorTheme: {
+            name: 'uniform',
+            params: {
+                value: color,
+                saturation: 0,
+                lightness: 0,
+            }
+        },
+        sizeTheme: {
+            name: 'physical',
+            params: {
+                scale: 1,
+            }
+        },
+    };
+}
+
+function getPlyShapeParams(color: Color, clipVariant: Clip.Variant) {
+    return {
+        ...PD.getDefaultValues(BaseGeometry.Params),
+        instanceGranularity: true,
+        ignoreLight: true,
+        clip: {
+            variant: clipVariant,
+            objects: [],
+        },
+        quality: 'custom',
+        doubleSided: true,
+        coloring: {
+            name: 'uniform',
+            params: { color }
+        },
+        grouping: {
+            name: 'none',
+            params: {}
+        },
+        material: {
+            metalness: 0.0,
+            roughness: 1.0,
+            bumpiness: 1.0,
+        },
+        bumpAmplitude: 0.1,
+        bumpFrequency: 0.1 / 10,
+    };
+}
+
+export async function createGenericHierarchy(plugin: PluginContext, file: Asset.File) {
+    const asset = await plugin.runTask(plugin.managers.asset.resolve(file, 'zip'));
+    let manifest: GenericManifest;
+    // TODO: remove special handling for martini prototype
+    if (asset.data['instanced_structure.json']) {
+        const d = asset.data['instanced_structure.json'];
+        const t = utf8Read(d, 0, d.length);
+        const martini = JSON.parse(t) as { model: string, positions: Vec3[], rotations: Vec3[], function: string }[];
+        console.log(martini);
+        manifest = martiniToGeneric(martini);
+    } else if (asset.data['manifest.json']) {
+        const d = asset.data['manifest.json'];
+        const t = utf8Read(d, 0, d.length);
+        manifest = JSON.parse(t) as GenericManifest;
+    } else {
+        throw new Error('no manifest found');
+    }
+    console.log(manifest);
+
+    const state = plugin.state.data;
+    const graphicsMode = MesoscaleState.get(plugin).graphics;
+    const groupParams = getMesoscaleGroupParams(graphicsMode);
+
+    async function addGroup(g: GenericGroup, cell: StateObjectSelector, parent: string) {
+        const group = await state.build()
+            .to(cell)
+            .apply(MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, description: g.description, color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
+            .commit();
+
+        if (g.children) {
+            for (const c of g.children) {
+                await addGroup(c, group, g.id);
+            }
+        }
+    }
+
+    for (const r of manifest.roots) {
+        const root = await state.build()
+            .toRoot()
+            .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, description: r.description, color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
+            .commit();
+
+        if (r.children) {
+            for (const c of r.children!) {
+                await addGroup(c, root, r.id);
+            }
+        }
+    }
+
+    const transformAssets = new Map<string, Asset>();
+    const getTransformAsset = (file: string) => {
+        if (!transformAssets.has(file)) {
+            const d = asset.data[file];
+            transformAssets.set(file, Asset.File(new File([d], file)));
+        }
+        return transformAssets.get(file)!;
+    };
+
+    const getAssetInstances = (instances: GenericInstances<string>): GenericInstances<Asset> => {
+        return {
+            positions: {
+                data: Array.isArray(instances.positions.data)
+                    ? instances.positions.data
+                    : {
+                        file: getTransformAsset(instances.positions.data.file),
+                        view: instances.positions.data.view,
+                    },
+                type: instances.positions.type,
+            },
+            rotations: {
+                data: Array.isArray(instances.rotations.data)
+                    ? instances.rotations.data
+                    : {
+                        file: getTransformAsset(instances.rotations.data.file),
+                        view: instances.rotations.data.view,
+                    },
+                variant: instances.rotations.variant,
+                type: instances.rotations.type,
+            }
+        };
+    };
+
+    await state.transaction(async () => {
+        try {
+            plugin.animationLoop.stop({ noDraw: true });
+            let build: StateBuilder.Root | StateBuilder.To<any> = state.build();
+            for (const ent of manifest.entities) {
+                const d = asset.data[ent.file];
+                const info = getFileNameInfo(ent.file);
+                const isBinary = ['bcif'].includes(info.ext);
+
+                const t = isBinary ? d : utf8Read(d, 0, d.length);
+                const file = Asset.File(new File([t], ent.file));
+
+                const color = (ent.color) ? Color.fromRgb(ent.color[0], ent.color[1], ent.color[2]) : ColorNames.skyblue;
+
+                const sizeFactor = ent.sizeFactor || 1;
+                const tags = ent.groups.map(({ id, root }) => `${root}:${id}`);
+                const instances = ent.instances && getAssetInstances(ent.instances);
+                const description = ent.description;
+
+                const label = ent.label || ent.file.split('.')[0];
+                build = build
+                    .toRoot()
+                    .apply(ReadFile, { file, label, isBinary });
+
+                if (['gro', 'cif', 'mmcif', 'mcif', 'bcif', 'pdb', 'ent', 'xyz', 'mol', 'sdf', 'sd', 'mol2'].includes(info.ext)) {
+                    if (['gro'].includes(info.ext)) {
+                        build = build.apply(TrajectoryFromGRO);
+                    } else if (['cif', 'mmcif', 'mcif', 'bcif'].includes(info.ext)) {
+                        build = build.apply(ParseCif).apply(TrajectoryFromMmCif);
+                    } else if (['pdb', 'ent'].includes(info.ext)) {
+                        build = build.apply(TrajectoryFromPDB);
+                    } else if (['xyz'].includes(info.ext)) {
+                        build = build.apply(TrajectoryFromXYZ);
+                    } else if (['mol'].includes(info.ext)) {
+                        build = build.apply(TrajectoryFromMOL);
+                    } else if (['sdf', 'sd'].includes(info.ext)) {
+                        build = build.apply(TrajectoryFromSDF);
+                    } else if (['mol2'].includes(info.ext)) {
+                        build = build.apply(TrajectoryFromMOL2);
+                    }
+
+                    let clipVariant: Clip.Variant = 'pixel';
+                    if (ent.instances) {
+                        if (Array.isArray(ent.instances.positions.data)) {
+                            clipVariant = ent.instances.positions.data.length <= 3 ? 'pixel' : 'instance';
+                        } else {
+                            const byteLength = ent.instances.positions.data.view
+                                ? ent.instances.positions.data.view.byteLength
+                                : asset.data[ent.instances.positions.data.file].length;
+                            clipVariant = byteLength <= 3 * 4 ? 'pixel' : 'instance';
+                        }
+                    }
+
+                    build = build
+                        .apply(ModelFromTrajectory, { modelIndex: 0 })
+                        .apply(StructureFromGeneric, { instances, label, description })
+                        .apply(StructureRepresentation3D, getSpacefillParams(color, sizeFactor, graphicsMode, clipVariant), { tags });
+                } else if (['ply'].includes(info.ext)) {
+                    if (['ply'].includes(info.ext)) {
+                        const transforms = await getTransforms(plugin, instances);
+                        const clipVariant = transforms.length === 1 ? 'pixel' : 'instance';
+                        build = build
+                            .apply(ParsePly)
+                            .apply(ShapeFromPly, { label, transforms })
+                            .apply(ShapeRepresentation3D, getPlyShapeParams(color, clipVariant), { tags });
+                    }
+                } else {
+                    console.warn(`unknown file format '${info.ext}'`);
+                }
+            }
+            await build.commit();
+        } catch (e) {
+            console.error(e);
+            plugin.log.error(e);
+        } finally {
+            plugin.animationLoop.start();
+        }
+    }).run();
+
+    asset.dispose();
+}
+
+//
+
+type GenericRoot = {
+    id: string
+    label?: string
+    description?: string
+    children: GenericGroup[]
+}
+
+type GenericGroup = {
+    id: string
+    /** reference to `${GenericRoot.id}` */
+    root: string
+    label?: string
+    description?: string
+    children?: GenericGroup[]
+}
+
+type GenericEntity = {
+    /**
+     * the entity file name
+     *
+     * the following extensions/formats are supported
+     *
+     * structures
+     * - gro
+     * - cif, mmcif, mcif, bcif
+     * - pdb, ent
+     * - xyz
+     * - mol
+     * - sdf, sd
+     * - mol2
+     *
+     * meshes
+     * - ply
+     */
+    file: string
+    label?: string
+    description?: string
+    color?: number[]
+    groups: {
+        /** reference to `${GenericGroup.id}` */
+        id: string,
+        /** reference to `${GenericGroup.root}` */
+        root: string
+    }[]
+    /**
+     * defaults to a single, untransformed instance
+     */
+    instances?: GenericInstances<string>
+    /**
+     * defaults to 1 (assuming fully atomic structures)
+     * for C-alpha only structures set to 2
+     * for Martini coarse-grained set to 1.5
+     */
+    sizeFactor?: number
+}
+
+type BinaryData<T extends string | Asset> = {
+    file: T,
+    view?: {
+        byteOffset: number,
+        byteLength: number
+    }
+}
+
+export type GenericInstances<T extends string | Asset> = {
+    /**
+     * translation vectors in Angstrom
+     * [x0, y0, z0, ..., xn, yn, zn] with n = count - 1
+     */
+    positions: {
+        /**
+         * either the data itself or a pointer to binary data
+         */
+        data: number[] | BinaryData<T>
+        /**
+         * how to interpret the data
+         * defaults to `{ kind: 'Array', type: 'Float32' }`
+         */
+        type?: { kind: 'Array', type: 'Float32' }
+        // TODO: maybe worthwhile in the future, mirroring encoders from BinaryCIF
+        // | { kind: 'IntegerPackedFixedPoint', byteCount: number, srcSize: number, factor: number, srcType: 'Float32' }
+    }
+    /**
+     * euler angles in XYZ order
+     * [x0, y0, z0, ..., xn, yn, zn] with n = count - 1
+     *
+     * quaternion rotations in XYZW order
+     * [x0, y0, z0, w0, ..., xn, yn, zn, wn] with n = count - 1
+     *
+     * rotation matrices in row-major order
+     * [m00_0, m01_0, m02_0, ..., m20_n, m21_n, m22_n] with n = count - 1
+     */
+    rotations: {
+        variant: 'euler' | 'quaternion' | 'matrix',
+        /**
+         * either the data itself or a pointer to binary data
+         */
+        data: number[] | BinaryData<T>
+        /**
+         * how to interpret the data
+         * defaults to `{ kind: 'Array', type: 'Float32' }`
+         */
+        type?: { kind: 'Array', type: 'Float32' }
+    }
+}
+
+type GenericFrame = {
+    time: number
+    entities: {
+        file: string
+        instances: GenericInstances<string>
+    }[]
+}
+
+type GenericTrajectory = {
+    label?: string
+    description?: string
+    frames: GenericFrame[]
+}
+
+type GenericManifest = {
+    label?: string
+    description?: string
+    roots: GenericRoot[]
+    entities: GenericEntity[]
+    trajectories?: GenericTrajectory[]
+}
+
+//
+
+const p = Vec3();
+const q = Quat();
+const m = Mat3();
+const e = Euler();
+
+async function getPositions(plugin: PluginContext, p: GenericInstances<Asset>['positions']): Promise<NumberArray> {
+    if (Array.isArray(p.data)) {
+        return p.data;
+    } else {
+        const a = await plugin.runTask(plugin.managers.asset.resolve(p.data.file, 'binary'));
+        const o = p.data.view?.byteOffset || 0;
+        const l = p.data.view?.byteLength || a.data.byteLength;
+        return new Float32Array(a.data.buffer, o + a.data.byteOffset, l / 4);
+    }
+};
+
+async function getRotations(plugin: PluginContext, r: GenericInstances<Asset>['rotations']): Promise<NumberArray> {
+    if (Array.isArray(r.data)) {
+        return r.data;
+    } else {
+        const a = await plugin.runTask(plugin.managers.asset.resolve(r.data.file, 'binary'));
+        const o = r.data.view?.byteOffset || 0;
+        const l = r.data.view?.byteLength || a.data.byteLength;
+        return new Float32Array(a.data.buffer, o + a.data.byteOffset, l / 4);
+    }
+};
+
+export async function getTransforms(plugin: PluginContext, instances?: GenericInstances<Asset>) {
+    const transforms: Mat4[] = [];
+    if (instances) {
+        const positions = await getPositions(plugin, instances.positions);
+        const rotations = await getRotations(plugin, instances.rotations);
+
+        for (let i = 0, il = positions.length / 3; i < il; ++i) {
+            Vec3.fromArray(p, positions, i * 3);
+            if (instances.rotations.variant === 'matrix') {
+                Mat3.fromArray(m, rotations, i * 9);
+                const t = Mat4.fromMat3(Mat4(), m);
+                Mat4.setTranslation(t, p);
+                transforms.push(t);
+            } else if (instances.rotations.variant === 'quaternion') {
+                Quat.fromArray(q, rotations, i * 4);
+                const t = Mat4.fromQuat(Mat4(), q);
+                Mat4.setTranslation(t, p);
+                transforms.push(t);
+            } else if (instances.rotations.variant === 'euler') {
+                Euler.fromArray(e, rotations, i * 3);
+                Quat.fromEuler(q, e, 'XYZ');
+                const t = Mat4.fromQuat(Mat4(), q);
+                Mat4.setTranslation(t, p);
+                transforms.push(t);
+            }
+        }
+    } else {
+        transforms.push(Mat4.identity());
+    }
+
+    return transforms;
+}
+
+//
+
+type MartiniManifest = {
+    model: string,
+    positions: Vec3[],
+    rotations: Vec3[],
+    function: string
+}[]
+
+function martiniToGeneric(martini: MartiniManifest): GenericManifest {
+    const functionRoot: GenericRoot = {
+        id: 'function',
+        label: 'Function',
+        description: 'Functional classification',
+        children: [],
+    };
+    const entities: GenericEntity[] = [];
+
+    const seenGroups = new Set<string>();
+
+    const membraneGroup = {
+        id: 'membane',
+        root: 'function',
+        label: 'Membrane',
+        children: [] as GenericGroup[],
+    };
+    functionRoot.children!.push(membraneGroup);
+    seenGroups.add(membraneGroup.id);
+
+    const lipidsGroup = {
+        id: 'lipid',
+        root: 'function',
+        label: 'Lipid',
+        children: [] as GenericGroup[],
+    };
+    membraneGroup.children!.push(lipidsGroup);
+    seenGroups.add(lipidsGroup.id);
+
+    const upperGroup = {
+        id: 'upper',
+        root: 'function',
+        label: 'Upper Leaflet',
+    };
+    lipidsGroup.children!.push(upperGroup);
+    seenGroups.add(upperGroup.id);
+
+    const lowerGroup = {
+        id: 'lower',
+        root: 'function',
+        label: 'Lower Leaflet',
+    };
+    lipidsGroup.children!.push(lowerGroup);
+    seenGroups.add(lowerGroup.id);
+
+    const memprotGroup = {
+        id: 'memprot',
+        root: 'function',
+        label: 'Transmembrane Protein',
+    };
+    membraneGroup.children!.push(memprotGroup);
+    seenGroups.add(memprotGroup.id);
+
+    for (const e of martini) {
+        const label = e.model.split('.')[0];
+        const group = e.function || 'Metabolite';
+
+        const positions = {
+            data: e.positions.flat().map(x => Math.round((x * 10) * 100) / 100)
+        };
+        const rotations = {
+            data: e.rotations.flat().map(x => Math.round(x * 100) / 100),
+            variant: 'euler' as const,
+        };
+
+        if (group.includes('lower leaflet')) {
+            entities.push({
+                file: e.model,
+                label: label.substring(15),
+                groups: [{ root: 'function', id: 'lower' }],
+                instances: { positions, rotations },
+                sizeFactor: 1.5,
+            });
+        } else if (group.includes('upper leaflet')) {
+            entities.push({
+                file: e.model,
+                label: label.substring(15),
+                groups: [{ root: 'function', id: 'upper' }],
+                instances: { positions, rotations },
+                sizeFactor: 1.5,
+            });
+        } else if (group.length === 4) {
+            entities.push({
+                file: e.model,
+                label: label.substring(17),
+                groups: [{ root: 'function', id: 'memprot' }],
+                instances: { positions, rotations },
+                sizeFactor: 1.5,
+            });
+        } else {
+            if (!seenGroups.has(group)) {
+                functionRoot.children!.push({
+                    id: group,
+                    root: 'function',
+                    label: group,
+                });
+                seenGroups.add(group);
+            }
+            entities.push({
+                file: e.model,
+                label,
+                groups: [{ root: 'function', id: group }],
+                instances: { positions, rotations },
+                sizeFactor: 1.5,
+            });
+        }
+    }
+
+    return {
+        label: 'Martini',
+        description: 'Martini coarse-grained model',
+        roots: [functionRoot],
+        entities,
+    };
+}

src/apps/mesoscale-explorer/data/mmcif/model.ts

@@ -0,0 +1,203 @@
+/**
+ * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { SortedArray } from '../../../../mol-data/int';
+import { SymmetryOperator } from '../../../../mol-math/geometry';
+import { Mat4 } from '../../../../mol-math/linear-algebra';
+import { ModelSymmetry } from '../../../../mol-model-formats/structure/property/symmetry';
+import { CustomStructureProperty } from '../../../../mol-model-props/common/custom-structure-property';
+import { ElementIndex, EntityIndex, Model, Structure, Unit } from '../../../../mol-model/structure';
+import { Assembly, Symmetry } from '../../../../mol-model/structure/model/properties/symmetry';
+import { PluginStateObject as PSO, PluginStateTransform } from '../../../../mol-plugin-state/objects';
+import { PluginContext } from '../../../../mol-plugin/context';
+import { StateTransformer } from '../../../../mol-state/transformer';
+import { Task } from '../../../../mol-task';
+import { deepEqual } from '../../../../mol-util';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { partitionUnits } from '../util';
+
+function createModelChainMap(model: Model) {
+    const builder = new Structure.StructureBuilder();
+    const units = new Map<string, Unit>();
+
+    const { label_asym_id, _rowCount } = model.atomicHierarchy.chains;
+    const { offsets } = model.atomicHierarchy.chainAtomSegments;
+
+    for (let i = 0; i < _rowCount; i++) {
+        const elements = SortedArray.ofBounds(offsets[i] as ElementIndex, offsets[i + 1] as ElementIndex);
+        const unit = builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements, Unit.Trait.FastBoundary);
+        units.set(label_asym_id.value(i), unit);
+    }
+
+    return units;
+}
+
+function buildAssembly(model: Model, assembly: Assembly) {
+    const coordinateSystem = SymmetryOperator.create(assembly.id, Mat4.identity(), { assembly: { id: assembly.id, operId: 0, operList: [] } });
+    const assembler = Structure.Builder({
+        coordinateSystem,
+        label: model.label,
+    });
+
+    const units = createModelChainMap(model);
+
+    for (const g of assembly.operatorGroups) {
+        for (const oper of g.operators) {
+            for (const id of g.asymIds!) {
+                const u = units.get(id);
+                if (u) {
+                    assembler.addWithOperator(u, oper);
+                } else {
+                    console.log(`missing asymId '${id}'`);
+                }
+            }
+        }
+    }
+
+    return assembler.getStructure();
+}
+
+export { MmcifAssembly };
+type MmcifAssembly = typeof MmcifAssembly
+const MmcifAssembly = PluginStateTransform.BuiltIn({
+    name: 'mmcif-assembly',
+    display: { name: 'Mmcif Assembly' },
+    from: PSO.Molecule.Model,
+    to: PSO.Molecule.Structure,
+    params: {
+        id: PD.Text('', { label: 'Asm Id', description: 'Assembly Id (use empty for the 1st assembly)' }),
+    }
+})({
+    canAutoUpdate({ newParams }) {
+        return true;
+    },
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Build Structure', async ctx => {
+            const model = a.data;
+
+            let id = params.id;
+            let asm: Assembly | undefined = void 0;
+            const symmetry = ModelSymmetry.Provider.get(model);
+
+            // if no id is specified, use the 1st assembly.
+            if (!id && symmetry && symmetry.assemblies.length !== 0) {
+                id = symmetry.assemblies[0].id;
+            }
+
+            if (!symmetry || symmetry.assemblies.length === 0) {
+                plugin.log.warn(`Model '${model.entryId}' has no assembly, returning model structure.`);
+            } else {
+                asm = Symmetry.findAssembly(model, id || '');
+                if (!asm) {
+                    plugin.log.warn(`Model '${model.entryId}' has no assembly called '${id}', returning model structure.`);
+                }
+            }
+
+            const base = Structure.ofModel(model);
+            if (!asm) {
+                const label = { label: 'Model', description: Structure.elementDescription(base) };
+                return new PSO.Molecule.Structure(base, label);
+            }
+
+            const s = buildAssembly(model, asm);
+
+            const objProps = { label: `Assembly ${id}`, description: Structure.elementDescription(s) };
+            return new PSO.Molecule.Structure(s, objProps);
+        });
+    },
+    update({ newParams, oldParams }) {
+        return deepEqual(newParams, oldParams)
+            ? StateTransformer.UpdateResult.Unchanged
+            : StateTransformer.UpdateResult.Recreate;
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});
+
+type UnitsByEntity = Map<EntityIndex, Unit[]>;
+const UnitsByEntity = CustomStructureProperty.createSimple<UnitsByEntity>('units_by_entity', 'root');
+
+function getUnitsByEntity(structure: Structure): UnitsByEntity {
+    if (UnitsByEntity.get(structure).value) {
+        return UnitsByEntity.get(structure).value!;
+    }
+
+    const atomicIndex = structure.model.atomicHierarchy.index;
+    const spheresIndex = structure.model.coarseHierarchy.spheres;
+    const map: UnitsByEntity = new Map();
+    for (const ug of structure.unitSymmetryGroups) {
+        const u = ug.units[0];
+        let e: EntityIndex;
+        if (Unit.isAtomic(u)) {
+            e = atomicIndex.getEntityFromChain(u.chainIndex[u.elements[0]]);
+        } else if (Unit.isSpheres(u)) {
+            e = spheresIndex.getEntityFromChain(u.coarseElements.chainElementSegments.index[u.elements[0]]);
+        } else {
+            continue;
+        }
+
+        if (!map.has(e)) map.set(e, []);
+        const entityUnits = map.get(e)!;
+
+        for (let i = 0, il = ug.units.length; i < il; ++i) {
+            entityUnits.push(ug.units[i]);
+        }
+    }
+
+    UnitsByEntity.set(structure, { value: map }, map);
+    return map;
+}
+
+export { MmcifStructure };
+type MmcifStructure = typeof MmcifStructure
+const MmcifStructure = PluginStateTransform.BuiltIn({
+    name: 'mmcif-structure',
+    display: { name: 'Mmcif Structure' },
+    from: PSO.Root,
+    to: PSO.Molecule.Structure,
+    params: {
+        structureRef: PD.Text(''),
+        entityId: PD.Text(''),
+        cellSize: PD.Numeric(500, { min: 0, max: 10000, step: 100 }),
+    }
+})({
+    canAutoUpdate({ newParams }) {
+        return true;
+    },
+    apply({ a, params, dependencies }) {
+        return Task.create('Build Structure', async ctx => {
+            const parent = dependencies![params.structureRef].data as Structure;
+            const { entities } = parent.model;
+            const idx = entities.getEntityIndex(params.entityId);
+
+            const unitsByEntity = getUnitsByEntity(parent);
+            const units = unitsByEntity.get(idx) || [];
+            const unitCount = units.length;
+
+            let structure: Structure;
+            if (unitCount > 1 && units.every(u => u.conformation.operator.isIdentity)) {
+                const mergedUnits = partitionUnits(units, params.cellSize);
+                structure = Structure.create(mergedUnits);
+            } else {
+                structure = Structure.create(units);
+            }
+            // could also use _struct_ref.pdbx_db_accession to point to uniprot with _struct_ref.db_name == UNP
+            const label = entities.data.pdbx_description.value(idx).join(', ') || 'model';
+            const description = `*Entity id* ${entities.data.id.value(idx)} *src_method* ${entities.data.src_method.value(idx)} *type* ${entities.data.type.value(idx)}`;
+            return new PSO.Molecule.Structure(structure, { label, description: description });
+        });
+    },
+    update({ newParams, oldParams }) {
+        return deepEqual(newParams, oldParams)
+            ? StateTransformer.UpdateResult.Unchanged
+            : StateTransformer.UpdateResult.Recreate;
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});

src/apps/mesoscale-explorer/data/mmcif/preset.ts

@@ -0,0 +1,191 @@
+/**
+ * Copyright (c) 2023-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { Model } from '../../../../mol-model/structure/model/model';
+import { PluginStateObject } from '../../../../mol-plugin-state/objects';
+import { StructureRepresentation3D } from '../../../../mol-plugin-state/transforms/representation';
+import { PluginContext } from '../../../../mol-plugin/context';
+import { SpacefillRepresentationProvider } from '../../../../mol-repr/structure/representation/spacefill';
+import { StateObjectRef, StateObjectSelector, StateBuilder } from '../../../../mol-state';
+import { Clip } from '../../../../mol-util/clip';
+import { Color } from '../../../../mol-util/color';
+import { ColorNames } from '../../../../mol-util/color/names';
+import { GraphicsMode, MesoscaleGroup, MesoscaleState, getDistinctBaseColors, getDistinctGroupColors, getGraphicsModeProps, getMesoscaleGroupParams } from '../state';
+import { MmcifAssembly, MmcifStructure } from './model';
+
+function getSpacefillParams(color: Color, scaleFactor: number, graphics: GraphicsMode, clipVariant: Clip.Variant) {
+    const gmp = getGraphicsModeProps(graphics === 'custom' ? 'quality' : graphics);
+    return {
+        type: {
+            name: 'spacefill',
+            params: {
+                ...SpacefillRepresentationProvider.defaultValues,
+                ignoreHydrogens: false,
+                instanceGranularity: false,
+                ignoreLight: true,
+                lodLevels: gmp.lodLevels.map(l => {
+                    return {
+                        ...l,
+                        stride: Math.max(1, Math.round(l.stride / Math.pow(scaleFactor, l.scaleBias)))
+                    };
+                }),
+                quality: 'lowest', // avoid 'auto', triggers boundary calc
+                clip: {
+                    variant: clipVariant,
+                    objects: [],
+                },
+                clipPrimitive: true,
+                approximate: gmp.approximate,
+                alphaThickness: gmp.alphaThickness,
+                interior: {
+                    color: Color.fromNormalizedRgb(0, 0, 0),
+                    colorStrength: 0.15,
+                    substance: { metalness: 0.0, roughness: 1.0, bumpiness: 0.0 },
+                    substanceStrength: 1,
+                }
+            },
+        },
+        colorTheme: {
+            name: 'uniform',
+            params: {
+                value: color,
+                saturation: 0,
+                lightness: 0,
+            }
+        },
+        sizeTheme: {
+            name: 'physical',
+            params: {
+                scale: scaleFactor,
+            }
+        },
+    };
+}
+
+export async function createMmcifHierarchy(plugin: PluginContext, trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>) {
+    const builder = plugin.builders.structure;
+    const state = plugin.state.data;
+
+    const model = await builder.createModel(trajectory, { modelIndex: 0 });
+    const { data: entities, subtype } = model.data!.entities;
+
+    const sd = model.data?.sourceData;
+    if (MmcifFormat.is(sd)) {
+        const pdbId = sd.data.db.struct.entry_id.value(0);
+        MesoscaleState.set(plugin, {
+            description: sd.data.db.struct.title.value(0),
+            link: pdbId ? `https://www.rcsb.org/structure/${pdbId}` : ''
+        });
+    }
+
+    const spheresAvgRadius = new Map<string, number>();
+    if (model.data!.coarseHierarchy.isDefined) {
+        const spheresCount = new Map<string, number>();
+        const spheresEntity_id = model.data!.coarseHierarchy.spheres.entity_id;
+        const spheresRadius = model.data!.coarseConformation.spheres.radius;
+        for (let i = 0, il = spheresEntity_id.rowCount; i < il; ++i) {
+            const entitiId = spheresEntity_id.value(i);
+            const radius = spheresRadius[i];
+            if (!spheresCount.has(entitiId)) {
+                spheresCount.set(entitiId, 1);
+                spheresAvgRadius.set(entitiId, radius);
+            } else {
+                spheresCount.set(entitiId, spheresCount.get(entitiId)! + 1);
+                spheresAvgRadius.set(entitiId, spheresAvgRadius.get(entitiId)! + radius);
+            }
+        }
+        spheresAvgRadius.forEach((v, k) => {
+            spheresAvgRadius.set(k, v / spheresCount.get(k)!);
+        });
+    }
+
+    const coarseGrained = Model.isCoarseGrained(model.data!);
+
+    const entGroups = new Map<string, StateObjectSelector>();
+    const entIds = new Map<string, { idx: number, members: Map<number, number> }>();
+    const entColors = new Map<string, Color[]>();
+
+    const graphicsMode = MesoscaleState.get(plugin).graphics;
+    const groupParams = getMesoscaleGroupParams(graphicsMode);
+
+    const base = await state.build()
+        .to(model)
+        .apply(MmcifAssembly, { id: '' })
+        .commit();
+
+    const units = base.data!.units;
+    const willBeMerged = units.length > 1 && units.every(u => u.conformation.operator.isIdentity);
+    const clipVariant = willBeMerged ? 'pixel' : 'instance';
+
+    const entRoot = await state.build()
+        .toRoot()
+        .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: 'ent:', label: 'entity', color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .commit();
+
+    const getEntityType = (i: number) => {
+        if (entities.type.value(i) === 'water') return 'water' as const;
+        return subtype.value(i) || 'unknown type';
+    };
+
+    for (let i = 0; i < entities._rowCount; i++) {
+        const t = getEntityType(i);
+        if (!entIds.has(t)) {
+            entIds.set(t, { idx: entIds.size, members: new Map() });
+        }
+        const cm = entIds.get(t)!;
+        cm.members.set(i, cm.members.size);
+    }
+
+    //
+
+    const baseEntColors = getDistinctBaseColors(entIds.size, 0);
+    const entIdEntries = Array.from(entIds.entries());
+    for (let i = 0; i < entIdEntries.length; ++i) {
+        const [t, m] = entIdEntries[i];
+        const groupColors = getDistinctGroupColors(m.members.size, baseEntColors[i], 20, 0);
+        entColors.set(t, groupColors);
+    }
+
+    for (let i = 0; i < entities._rowCount; i++) {
+        const t = getEntityType(i);
+        if (!entGroups.has(t)) {
+            const colorIdx = entIds.get(t)?.idx;
+            const color = colorIdx !== undefined ? baseEntColors[colorIdx] : ColorNames.white;
+            const group = await state.build()
+                .to(entRoot)
+                .applyOrUpdateTagged(`group:ent:${t}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                .commit({ revertOnError: true });
+            entGroups.set(t, group);
+        }
+    }
+
+    //
+
+    await state.transaction(async () => {
+        try {
+            const dependsOn = [base.ref];
+            plugin.animationLoop.stop({ noDraw: true });
+            let build: StateBuilder.Root | StateBuilder.To<any> = state.build();
+            for (let i = 0; i < entities._rowCount; i++) {
+                const t = getEntityType(i);
+                const color = entColors.get(t)![entIds.get(t)!.members.get(i)!];
+                const scaleFactor = spheresAvgRadius.get(entities.id.value(i)) || (coarseGrained ? 2 : 1);
+
+                build = build
+                    .toRoot()
+                    .apply(MmcifStructure, { structureRef: base.ref, entityId: entities.id.value(i) }, { dependsOn })
+                    .apply(StructureRepresentation3D, getSpacefillParams(color, scaleFactor, graphicsMode, clipVariant), { tags: [`ent:${t}`] });
+            }
+            await build.commit();
+        } catch (e) {
+            console.error(e);
+            plugin.log.error(e);
+        } finally {
+            plugin.animationLoop.start();
+        }
+    }).run();
+}

src/apps/mesoscale-explorer/data/petworld/model.ts

@@ -0,0 +1,140 @@
+/**
+ * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mat4 } from '../../../../mol-math/linear-algebra/3d/mat4';
+import { getMatrices, operatorGroupsProvider } from '../../../../mol-model-formats/structure/property/assembly';
+import { Structure, StructureElement, StructureProperties, Trajectory, Unit } from '../../../../mol-model/structure';
+import { Assembly } from '../../../../mol-model/structure/model/properties/symmetry';
+import { PluginStateObject as SO, PluginStateTransform } from '../../../../mol-plugin-state/objects';
+import { Task } from '../../../../mol-task';
+import { Table } from '../../../../mol-data/db';
+import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { arrayFind } from '../../../../mol-data/util';
+import { StateObject, StateTransformer } from '../../../../mol-state';
+import { CifField } from '../../../../mol-io/reader/cif';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { mergeUnits } from '../util';
+import { deepEqual } from '../../../../mol-util';
+
+export { StructureFromPetworld };
+type StructureFromPetworld = typeof StructureFromPetworld
+const StructureFromPetworld = PluginStateTransform.BuiltIn({
+    name: 'structure-from-petworld',
+    display: { name: 'Structure from PetWorld', description: 'Create a molecular structure from PetWorld models.' },
+    from: SO.Molecule.Trajectory,
+    to: SO.Molecule.Structure,
+    params: {
+        modelIndex: PD.Numeric(0),
+        entityIds: PD.Value<string[]>([]),
+    }
+})({
+    apply({ a, params }) {
+        return Task.create('Build Structure', async ctx => {
+            const s = await buildModelsAssembly(a.data, '1', params.modelIndex, params.entityIds).runInContext(ctx);
+            if (!s || !MmcifFormat.is(s.model.sourceData)) return StateObject.Null;
+
+            const { frame } = s.model.sourceData.data;
+            const pdbx_model = frame.categories.pdbx_model.getField('name')!;
+            const pdbx_description = frame.categories.pdbx_model.getField('description')!;
+            const description = pdbx_description ? pdbx_description.str(params.modelIndex) : Structure.elementDescription(s);
+            const label = pdbx_model.str(params.modelIndex);
+            const props = { label, description: description };
+            return new SO.Molecule.Structure(s, props);
+        });
+    },
+    update({ newParams, oldParams }) {
+        return deepEqual(newParams, oldParams)
+            ? StateTransformer.UpdateResult.Unchanged
+            : StateTransformer.UpdateResult.Recreate;
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});
+
+function buildModelsAssembly(trajectory: Trajectory, asmName: string, modelIndex: number, entitiyIds: string[]) {
+    return Task.create('Build Models Assembly', async ctx => {
+        const model = await Task.resolveInContext(trajectory.getFrameAtIndex(modelIndex), ctx);
+        if (!MmcifFormat.is(model.sourceData)) return;
+
+        const { db, frame } = model.sourceData.data;
+        const PDB_model_num = frame.categories.pdbx_struct_assembly_gen.getField('PDB_model_num')!;
+
+        // hack to cache models assemblies
+        if (!(trajectory as any).__modelsAssemblies) {
+            (trajectory as any).__modelsAssemblies = createModelsAssemblies(db.pdbx_struct_assembly, db.pdbx_struct_assembly_gen as StructAssemblyGen, db.pdbx_struct_oper_list, PDB_model_num);
+        }
+        const modelsAssemblies = (trajectory as any).__modelsAssemblies as ModelsAssembly[];
+
+        const modelsAssembly = arrayFind(modelsAssemblies, ma => ma.assembly.id.toLowerCase() === asmName);
+        if (!modelsAssembly) throw new Error(`Models Assembly '${asmName}' is not defined.`);
+
+        const { assembly } = modelsAssembly;
+        const assembler = Structure.Builder();
+        const g = assembly.operatorGroups[modelIndex];
+
+        const structure = Structure.ofModel(model);
+        const l = StructureElement.Location.create(structure);
+        const units = structure.units.filter(u => {
+            l.unit = u;
+            l.element = u.elements[0];
+            return entitiyIds.includes(StructureProperties.entity.id(l));
+        });
+        const unit = mergeUnits(units, 0);
+
+        for (const oper of g.operators) {
+            assembler.addUnit(unit.kind, unit.model, oper, unit.elements, unit.traits | Unit.Trait.FastBoundary, unit.invariantId);
+        }
+
+        return assembler.getStructure();
+    });
+}
+
+//
+
+type StructAssembly = Table<mmCIF_Schema['pdbx_struct_assembly']>
+type StructAssemblyGen = Table<mmCIF_Schema['pdbx_struct_assembly_gen']>
+type StructOperList = Table<mmCIF_Schema['pdbx_struct_oper_list']>
+
+type ModelsAssembly = { assembly: Assembly, modelNums: number[] };
+
+function createModelsAssemblies(pdbx_struct_assembly: StructAssembly, pdbx_struct_assembly_gen: StructAssemblyGen, pdbx_struct_oper_list: StructOperList, PDB_model_num: CifField): ReadonlyArray<ModelsAssembly> {
+    if (!pdbx_struct_assembly._rowCount) return [];
+
+    const matrices = getMatrices(pdbx_struct_oper_list);
+    const assemblies: ModelsAssembly[] = [];
+    for (let i = 0; i < pdbx_struct_assembly._rowCount; i++) {
+        assemblies[assemblies.length] = createModelsAssembly(pdbx_struct_assembly, pdbx_struct_assembly_gen, i, matrices, PDB_model_num);
+    }
+    return assemblies;
+}
+
+type Matrices = Map<string, Mat4>
+type Generator = { assemblyId: string, expression: string, asymIds: string[] }
+
+function createModelsAssembly(pdbx_struct_assembly: StructAssembly, pdbx_struct_assembly_gen: StructAssemblyGen, index: number, matrices: Matrices, PDB_model_num: CifField): ModelsAssembly {
+    const id = pdbx_struct_assembly.id.value(index);
+    const details = pdbx_struct_assembly.details.value(index);
+    const generators: Generator[] = [];
+    const modelNums: number[] = [];
+
+    const { assembly_id, oper_expression, asym_id_list } = pdbx_struct_assembly_gen;
+
+    for (let i = 0, _i = pdbx_struct_assembly_gen._rowCount; i < _i; i++) {
+        if (assembly_id.value(i) !== id) continue;
+        generators[generators.length] = {
+            assemblyId: id,
+            expression: oper_expression.value(i),
+            asymIds: asym_id_list.value(i)
+        };
+        modelNums[modelNums.length] = PDB_model_num.int(i);
+    }
+
+    const assembly = Assembly.create(id, details, operatorGroupsProvider(generators, matrices));
+
+    return { assembly, modelNums };
+}

src/apps/mesoscale-explorer/data/petworld/preset.ts

@@ -0,0 +1,140 @@
+/**
+ * Copyright (c) 2022-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StateBuilder, StateObjectRef } from '../../../../mol-state';
+import { StructureFromPetworld } from './model';
+import { Color } from '../../../../mol-util/color';
+import { SpacefillRepresentationProvider } from '../../../../mol-repr/structure/representation/spacefill';
+import { StructureRepresentation3D } from '../../../../mol-plugin-state/transforms/representation';
+import { PluginContext } from '../../../../mol-plugin/context';
+import { PluginStateObject } from '../../../../mol-plugin-state/objects';
+import { GraphicsMode, MesoscaleGroup, MesoscaleState, getDistinctBaseColors, getGraphicsModeProps, getMesoscaleGroupParams } from '../state';
+import { ColorNames } from '../../../../mol-util/color/names';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { Task } from '../../../../mol-task';
+
+function getSpacefillParams(color: Color, graphics: GraphicsMode) {
+    const gmp = getGraphicsModeProps(graphics === 'custom' ? 'quality' : graphics);
+    return {
+        type: {
+            name: 'spacefill',
+            params: {
+                ...SpacefillRepresentationProvider.defaultValues,
+                ignoreHydrogens: true,
+                instanceGranularity: true,
+                ignoreLight: true,
+                lodLevels: gmp.lodLevels,
+                quality: 'lowest', // avoid 'auto', triggers boundary calc
+                clip: {
+                    variant: 'instance',
+                    objects: [],
+                },
+                clipPrimitive: true,
+                approximate: gmp.approximate,
+                alphaThickness: gmp.alphaThickness,
+                interior: {
+                    color: Color.fromNormalizedRgb(0, 0, 0),
+                    colorStrength: 0.15,
+                    substance: { metalness: 0.0, roughness: 1.0, bumpiness: 0.0 },
+                    substanceStrength: 1,
+                }
+            },
+        },
+        colorTheme: {
+            name: 'uniform',
+            params: {
+                value: color,
+                saturation: 0,
+                lightness: 0,
+            }
+        },
+        sizeTheme: {
+            name: 'physical',
+            params: {
+                scale: 1,
+            }
+        },
+    };
+}
+
+export async function createPetworldHierarchy(plugin: PluginContext, trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>) {
+    const cell = StateObjectRef.resolveAndCheck(plugin.state.data, trajectory);
+    const tr = cell?.obj?.data;
+    if (!cell || !tr) return;
+
+    if (!MmcifFormat.is(tr.representative.sourceData)) return;
+
+    const membrane: { modelIndex: number, entityIds: string[] }[] = [];
+    const other: { modelIndex: number, entityIds: string[] }[] = [];
+    for (let i = 0; i < tr.frameCount; ++i) {
+        const m = await Task.resolveInContext(tr.getFrameAtIndex(i));
+        // cannot use m.properties.structAsymMap because petworld models
+        // may assign the same asymId to multiple entities
+        const { label_asym_id, label_entity_id, _rowCount } = m.atomicHierarchy.chains;
+        const membraneIds: string[] = [];
+        const otherIds: string[] = [];
+        const seen = new Set<string>();
+        for (let i = 0; i < _rowCount; i ++) {
+            const entityId = label_entity_id.value(i);
+            if (seen.has(entityId)) continue;
+
+            const asymId = label_asym_id.value(i);
+            if (asymId.startsWith('MEM')) {
+                membraneIds.push(entityId);
+            } else {
+                otherIds.push(entityId);
+            }
+            seen.add(entityId);
+        }
+        if (membraneIds.length) {
+            membrane.push({ modelIndex: i, entityIds: membraneIds });
+        }
+        if (otherIds.length) {
+            other.push({ modelIndex: i, entityIds: otherIds });
+        }
+    }
+
+    const state = plugin.state.data;
+    const graphicsMode = MesoscaleState.get(plugin).graphics;
+    const groupParams = getMesoscaleGroupParams(graphicsMode);
+
+    const group = await state.build()
+        .toRoot()
+        .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: ['group:ent:'], state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .commit({ revertOnError: true });
+
+    await state.build()
+        .to(group)
+        .apply(MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', illustrative: false, value: ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: ['group:ent:mem', 'ent:', '__no_group_color__'], state: { isCollapsed: true, isHidden: groupParams.hidden } })
+        .commit();
+
+    const colors = getDistinctBaseColors(other.length, 0);
+
+    await state.transaction(async () => {
+        try {
+            plugin.animationLoop.stop({ noDraw: true });
+            let build: StateBuilder.Root | StateBuilder.To<any> = state.build();
+            for (let i = 0, il = membrane.length; i < il; ++i) {
+                build = build
+                    .to(cell)
+                    .apply(StructureFromPetworld, membrane[i])
+                    .apply(StructureRepresentation3D, getSpacefillParams(ColorNames.lightgrey, graphicsMode), { tags: ['ent:mem', '__no_group_color__'] });
+            }
+            for (let i = 0, il = other.length; i < il; ++i) {
+                build = build
+                    .to(cell)
+                    .apply(StructureFromPetworld, other[i])
+                    .apply(StructureRepresentation3D, getSpacefillParams(colors[i], graphicsMode), { tags: ['ent:'] });
+            }
+            await build.commit();
+        } catch (e) {
+            console.error(e);
+            plugin.log.error(e);
+        } finally {
+            plugin.animationLoop.start();
+        }
+    }).run();
+}