4.3.0

* await the the snapshot setting to avoid rendering while applying snapshot. Request : export animation should take in account the trackball controller of 'rock' or 'spin' as well.

* add the updateController option when renderiing snapshot, camera rock and spin are thus taking into account

* forgot a file

* update the canvas3d using the current snapshot to allow camera rock and spin animation rendering

* changelog

.eslintignore

@@ -1,3 +1,4 @@
 node_modules/*
 build/*
+docs/site/*
 lib/*

.eslintrc.json

@@ -18,7 +18,7 @@
         ],
         "brace-style": "off",
         "comma-spacing": "off",
-        "space-infix-ops": "error",
+        "space-infix-ops": "off",
         "comma-dangle": "off",
         "eqeqeq": [
             "error",
@@ -31,7 +31,32 @@
         "no-unsafe-finally": "warn",
         "no-var": "error",
         "spaced-comment": "error",
-        "semi": "warn"
+        "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",
+        "no-constant-binary-expression": "error"
     },
     "overrides": [
         {
@@ -82,7 +107,15 @@
                     "error",
                     "1tbs", { "allowSingleLine": true }
                 ],
-                "@typescript-eslint/comma-spacing": "error"
+                "@typescript-eslint/comma-spacing": "error",
+                "@typescript-eslint/space-infix-ops": "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"]
             }
         }
     ]

.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/lint.yml

@@ -1,18 +0,0 @@
-on:
-  push:
-  pull_request:
-
-jobs:
-  eslint:
-    name: eslint
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v1
-    - name: install node v12
-      uses: actions/setup-node@v1
-      with:
-        node-version: 12
-    - name: yarn install
-      run: yarn install
-    - name: eslint
-      uses: icrawl/action-eslint@v1

.github/workflows/node.yml

@@ -0,0 +1,24 @@
+name: Build
+
+on:
+  push:
+    branches: master
+  pull_request:
+    branches: master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-node@v2
+      with:
+        node-version: 18
+    - run: npm ci
+    - run: sudo apt-get install xvfb
+    - name: Lint
+      run: npm run lint
+    - name: Test
+      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 +1,6 @@
 build/
 lib/
+docs/site/
 
 node_modules/
 debug.log
@@ -9,3 +10,5 @@ tsconfig.commonjs.tsbuildinfo
 
 *.sublime-workspace
 .idea
+
+.DS_Store

.npmignore

@@ -1 +1,5 @@
-tsconfig.commonjs.buildinfo
+tests
+perf-tests
+_spec
+*.tsbuildinfo
+*.js.map

.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

@@ -7,6 +7,8 @@
         "*.gql.ts": "graphql"
     },
     "eslint.options": {
-        "ignorePattern": ["webpack.config.js", "scripts/*"],
+        "overrideConfig": {
+            "ignorePatterns": ["webpack.config.js", "scripts/*"],
+        },
     }
 }

CITATION.cff

@@ -0,0 +1,72 @@
+cff-version: 1.2.0
+title: >-
+  Mol* library
+message: >-
+  Please cite this software using the metadata from
+  'preferred-citation'.
+authors:
+  - given-names: Alexander S
+    family-names: Rose
+    orcid: 'https://orcid.org/0000-0002-0893-5551'
+  - given-names: David
+    family-names: Sehnal
+    orcid: 'https://orcid.org/0000-0002-0682-3089'
+  - given-names: Sebastian
+    family-names: Bittrich
+    orcid: 'https://orcid.org/0000-0003-3576-0387'
+  - given-names: Áron Samuel
+    family-names: Kovács
+  - given-names: Ludovic
+    family-names: Autin
+    orcid: 'https://orcid.org/0000-0002-2197-191X'
+  - given-names: Michal
+    family-names: Malý
+  - given-names: Jiří
+    family-names: Černý
+  - given-names: Panagiotis
+    family-names: Tourlas
+type: software
+doi: 10.5281/zenodo.3947306
+preferred-citation:
+  authors:
+    - given-names: David
+      family-names: Sehnal
+      orcid: 'https://orcid.org/0000-0002-0682-3089'
+    - given-names: Sebastian
+      family-names: Bittrich
+      orcid: 'https://orcid.org/0000-0003-3576-0387'
+    - given-names: Mandar
+      family-names: Deshpande
+      orcid: 'https://orcid.org/0000-0002-9043-7665'
+    - given-names: Radka
+      family-names: Svobodová
+      orcid: 'https://orcid.org/0000-0002-3840-8760'
+    - given-names: Karel
+      family-names: Berka
+      orcid: 'https://orcid.org/0000-0001-9472-2589'
+    - given-names: Václav
+      family-names: Bazgier
+      orcid: 'https://orcid.org/0000-0003-3393-3010'
+    - given-names: Sameer
+      family-names: Velankar
+      orcid: 'https://orcid.org/0000-0002-8439-5964'
+    - given-names: Stephen K
+      family-names: Burley
+      orcid: 'https://orcid.org/0000-0002-2487-9713'
+    - given-names: Jaroslav
+      family-names: Koča
+      orcid: 'https://orcid.org/0000-0002-2780-4901'
+    - given-names: Alexander S
+      family-names: Rose
+      orcid: 'https://orcid.org/0000-0002-0893-5551'
+  title: >-
+    Mol* Viewer: modern web app for 3D visualization
+    and analysis of large biomolecular structures
+  type: article
+  doi: 10.1093/nar/gkab314
+  journal: "Nucleic Acids Research"
+  issue: W1
+  volume: 49
+  year: 2021
+  month: 7
+  pages: "W431–W437"

README.md

@@ -1,19 +1,26 @@
 [![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*
 
-The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will serve as a basis for the next-generation data delivery and analysis tools for macromolecular structure data. This is a collaboration between PDBe and RCSB PDB teams and the development will be open-source and available to anyone who wants to use it for developing visualization tools for macromolecular structure data available from [PDB](https://www.wwpdb.org/) and other institutions.
+The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of [LiteMol](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (developed by RCSB PDB) viewers.
 
-This particular project is the implementation of this technology (still under development).
+When using Mol*, please cite:
 
-*If you are looking for the "MOLeculAR structure annoTator", that package is now available on NPM as [MolArt](https://www.npmjs.com/package/molart).*
+David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: [Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures](https://doi.org/10.1093/nar/gkab314), *Nucleic Acids Research*, 2021; https://doi.org/10.1093/nar/gkab314.
 
-## Project Overview
+### Protein Data Bank Integrations
 
-The core of Mol* currently consists of these modules (see under `src/`):
+- The [pdbe-molstar](https://github.com/molstar/pdbe-molstar) library is the Mol* implementation used by EMBL-EBI data resources such as [PDBe](https://pdbe.org/), [PDBe-KB](https://pdbe-kb.org/) and [AlphaFold DB](https://alphafold.ebi.ac.uk/). This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.
+
+- [rcsb-molstar](https://github.com/molstar/rcsb-molstar) is the Mol* plugin used by [RCSB PDB](https://www.rcsb.org). The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, [rcsb-molstar](https://github.com/molstar/rcsb-molstar) allows to interactively add or hide of (parts of) chains, as seen in the [3D Protein Feature View](https://www.rcsb.org/3d-sequence/4hhb).
+
+
+## Project Structure Overview
+
+The core of Mol* consists of these modules (see under `src/`):
 
 - `mol-task` Computation abstraction with progress tracking and cancellation support.
 - `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
@@ -29,7 +36,6 @@ The core of Mol* currently consists of these modules (see under `src/`):
 - `mol-gl` A wrapper around WebGL.
 - `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
 - `mol-state` State representation tree with state saving and automatic updates.
-- `mol-app` Components for building UIs.
 - `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
 - `mol-plugin-state` State transformations, builders, and managers.
 - `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
@@ -41,7 +47,7 @@ Moreover, the project contains the implementation of `servers`, including
 - `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
 - `servers/plugin-state` A basic server to store Mol* Plugin states.
 
-The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+The project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
 
 ## Previous Work
 This project builds on experience from previous solutions:
@@ -69,6 +75,17 @@ If working on just the viewer, ``npm run watch-viewer`` will provide shorter com
 
 Debug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.
 
+### Cleaning and forcing a full rebuild
+    npm run clean
+
+Wipes the `build` and `lib` directories and `.tsbuildinfo` files.
+
+    npm run rebuild
+
+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.
+
 ### Build for production:
     NODE_ENV=production npm run build
 
@@ -103,10 +120,9 @@ and navigate to `build/viewer`
 
     node --max-old-space-size=4096 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=4096 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts
 
 ### Other scripts
 **Create chem comp bond table**
@@ -121,16 +137,21 @@ 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/servers/model/preprocess -i file.cif -ob file.bcif
+    node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
 
-To see all available commands, use ``node lib/servers/model/preprocess -h``.
+To see all available commands, use ``node lib/commonjs/servers/model/preprocess -h``.
 
 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
@@ -142,13 +163,12 @@ 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
@@ -169,12 +189,9 @@ To get syntax highlighting for shader and graphql files add the following to Vis
 ## Contributing
 Just open an issue or make a pull request. All contributions are welcome.
 
-## Roadmap
-Continually develop this prototype project. As individual modules become stable, make them into standalone libraries.
-
 ## Funding
 Funding sources include but are not limited to:
 * [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
 * [PDBe, EMBL-EBI](https://pdbe.org)
 * [CEITEC](https://www.ceitec.eu/)
-* [EntosAI](https://www.entos.ai) (``alpha-orbitals`` extension)
+* [EntosAI](https://www.entos.ai)

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

@@ -2,11 +2,11 @@ audit.block_doi
 
 database_code.depnum_ccdc_archive
 database_code.depnum_ccdc_fiz
-database_code.ICSD
-database_code.MDF
-database_code.NBS
-database_code.CSD
-database_code.COD
+database_code.icsd
+database_code.mdf
+database_code.nbs
+database_code.csd
+database_code.cod
 
 chemical.name_systematic
 chemical.name_common
@@ -24,8 +24,8 @@ atom_type_scat.dispersion_imag
 atom_type_scat.source
 
 space_group.crystal_system
-space_group.name_H-M_full
-space_group.IT_number
+space_group.name_h-m_full
+space_group.it_number
 space_group_symop.operation_xyz
 
 cell.length_a
@@ -35,14 +35,14 @@ cell.angle_alpha
 cell.angle_beta
 cell.angle_gamma
 cell.volume
-cell.formula_units_Z
+cell.formula_units_z
 
 atom_site.label
 atom_site.type_symbol
 atom_site.fract_x
 atom_site.fract_y
 atom_site.fract_z
-atom_site.U_iso_or_equiv
+atom_site.u_iso_or_equiv
 atom_site.adp_type
 atom_site.occupancy
 atom_site.calc_flag
@@ -52,20 +52,13 @@ atom_site.disorder_group
 atom_site.site_symmetry_multiplicity
 
 atom_site_aniso.label
-atom_site_aniso.U
-atom_site_aniso.U_11
-atom_site_aniso.U_22
-atom_site_aniso.U_33
-atom_site_aniso.U_23
-atom_site_aniso.U_13
-atom_site_aniso.U_12
-atom_site_aniso.U_su
-atom_site_aniso.U_11_su
-atom_site_aniso.U_22_su
-atom_site_aniso.U_33_su
-atom_site_aniso.U_23_su
-atom_site_aniso.U_13_su
-atom_site_aniso.U_12_su
+atom_site_aniso.u
+atom_site_aniso.u_11
+atom_site_aniso.u_22
+atom_site_aniso.u_33
+atom_site_aniso.u_23
+atom_site_aniso.u_13
+atom_site_aniso.u_12
 
 geom_bond.atom_site_label_1
 geom_bond.atom_site_label_2

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

@@ -24,6 +24,11 @@ atom_site.auth_asym_id
 atom_site.auth_seq_id
 atom_site.pdbx_PDB_model_num
 atom_site.ihm_model_id
+atom_site.pdbx_label_index
+atom_site.pdbx_sifts_xref_db_name
+atom_site.pdbx_sifts_xref_db_acc
+atom_site.pdbx_sifts_xref_db_num
+atom_site.pdbx_sifts_xref_db_res
 
 atom_site_anisotrop.id
 atom_site_anisotrop.U
@@ -246,6 +251,14 @@ citation_author.ordinal
 exptl.entry_id
 exptl.method
 
+software.classification
+software.date
+software.description
+software.name
+software.pdbx_ordinal
+software.type
+software.version
+
 struct.entry_id
 struct.title
 struct.pdbx_descriptor
@@ -802,4 +815,58 @@ ihm_multi_state_modeling.population_fraction_sd
 ihm_multi_state_modeling.state_type
 ihm_multi_state_modeling.state_name
 ihm_multi_state_modeling.experiment_type
-ihm_multi_state_modeling.details
+ihm_multi_state_modeling.details
+
+ma_data.content_type
+ma_data.content_type_other_details
+ma_data.id
+ma_data.name
+
+ma_model_list.data_id
+ma_model_list.model_group_id
+ma_model_list.model_group_name
+ma_model_list.model_id
+ma_model_list.model_name
+ma_model_list.model_type
+ma_model_list.ordinal_id
+
+ma_qa_metric.id
+ma_qa_metric.mode
+ma_qa_metric.name
+ma_qa_metric.software_group_id
+ma_qa_metric.type
+
+ma_qa_metric_global.metric_id
+ma_qa_metric_global.metric_value
+ma_qa_metric_global.model_id
+ma_qa_metric_global.ordinal_id
+
+ma_qa_metric_local.label_asym_id
+ma_qa_metric_local.label_comp_id
+ma_qa_metric_local.label_seq_id
+ma_qa_metric_local.metric_id
+ma_qa_metric_local.metric_value
+ma_qa_metric_local.model_id
+ma_qa_metric_local.ordinal_id
+
+ma_software_group.group_id
+ma_software_group.ordinal_id
+ma_software_group.software_id
+
+ma_target_entity.data_id
+ma_target_entity.entity_id
+ma_target_entity.origin
+
+ma_target_entity_instance.asym_id
+ma_target_entity_instance.details
+ma_target_entity_instance.entity_id
+
+ma_target_ref_db_details.db_accession
+ma_target_ref_db_details.db_code
+ma_target_ref_db_details.db_name
+ma_target_ref_db_details.ncbi_taxonomy_id
+ma_target_ref_db_details.organism_scientific
+ma_target_ref_db_details.seq_db_align_begin
+ma_target_ref_db_details.seq_db_align_end
+ma_target_ref_db_details.seq_db_isoform
+ma_target_ref_db_details.target_entity_id

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 |
+
+```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-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](./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. |
+| `--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/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 ([runVisualizeTunnels](../../../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 ([runVisualizeTunnel](../../../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 build
+```
+
+--------------------
+
+For a watch task to automatically rebuild the source code on changes, run
+
+```
+npm run watch
+```
+
+or if working just with the Viewer app for better performance
+
+```
+npm run watch-viewer
+```

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)
@@ -13,6 +15,7 @@
     * 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)
@@ -25,4 +28,24 @@
 * 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)
+* NOS bridges (LYS-CSO in 7B0L, 6ZWJ, 6ZWH)
+* Non-polymer components in polymer entities
+    * PN2 in 1F80
+    * ACE (many, e.g. 5AGU, 1E1X)
+    * ACY in 7ABY
+    * NH2 (many, e.g. 6Y13)
+* 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)

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 +1,274 @@
+# 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/context.ts#L71) 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 much 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 and options.
+
+Example usage without using WebPack:
+
+```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>
+```
+
+When using WebPack (or possibly other build tool) with the Mol* NPM package installed, the viewer class can be imported using 
+
+```ts
+import { Viewer } from 'molstar/build/viewer/molstar'
+
+function initViewer(target: string | HTMLElement) {
+    return new Viewer(target, { /* options */})
+}
+```
+
+## ``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(() => {
+    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 (!plugin.initViewer(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/selections.md

@@ -0,0 +1,110 @@
+# Selections
+
+
+Assuming you have a model already loaded into the plugin (see [Creating Plugin Instance](./instance.md)), these are some of the following method you can select structural data.
+
+### Selecting directly from the `hierarchy` manager
+
+One can 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 callbacks
+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);
+  }
+)
+```
+
+### `Molscript` language
+
+Molscript 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)).
+
+### 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. 
+ 
+### 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);
+```

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 +1,59 @@
+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://polyfill.io/v3/polyfill.min.js?features=es6
+  - 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
+    - Selections: 'plugin/selections.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'
+    - State Transforms:
+      - Custom Trajectory: 'plugin/transforms/custom-trajectory.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'
+  - Misc:
+    - Interesting PDB entries: misc/interesting-pdb-entries.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.

examples/ace2-hit.mol2

@@ -0,0 +1,86 @@
+@<TRIPOS>MOLECULE
+ace2_r_r2.top2000.poses.plain/3_Z1137565832_1_T2.pdb
+ 37 41 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1  C         64.7720   85.9180   38.1090 C.3     1  LIG1        0.0799
+      2  C         64.6440   84.6900   37.1570 C.3     1  LIG1        0.0306
+      3  C         65.2660   83.4260   37.8080 C.3     1  LIG1        0.0927
+      4  N         66.6560   83.6710   38.1790 N.pl3   1  LIG1       -0.2919
+      5  C         67.7080   82.9280   37.6260 C.ar    1  LIG1        0.1520
+      6  C         69.0970   83.1860   37.8250 C.ar    1  LIG1        0.0393
+      7  C         70.0830   82.4100   37.1810 C.ar    1  LIG1        0.0436
+      8  C         69.6450   81.3740   36.3510 C.ar    1  LIG1        0.1867
+      9  N         70.3370   80.5030   35.6050 N.ar    1  LIG1       -0.1270
+     10  N         69.4700   79.7480   35.0040 N.ar    1  LIG1       -0.1228
+     11  C         68.2200   80.1120   35.3570 C.ar    1  LIG1        0.2583
+     12  N         68.3350   81.1470   36.2040 N.ar    1  LIG1       -0.1866
+     13  N         67.4230   81.8700   36.8030 N.ar    1  LIG1       -0.1473
+     14  C         66.8190   84.7600   39.1350 C.3     1  LIG1        0.0927
+     15  C         66.2560   86.0870   38.5570 C.3     1  LIG1        0.0306
+     16  N         64.4520   87.4670   36.2150 N.am    1  LIG1       -0.2979
+     17  H         64.9740   86.7650   35.7110 H       1  LIG1        0.1498
+     18  C         64.2290   87.1720   37.5220 C.2     1  LIG1        0.2224
+     19  O         63.5690   87.9550   38.2480 O.2     1  LIG1       -0.2751
+     20  C         64.0160   88.6470   35.5420 C.3     1  LIG1        0.1559
+     21  C         65.9650   88.2170   32.5700 C.ar    1  LIG1        0.1629
+     22  N         65.8040   88.0390   33.8860 N.ar    1  LIG1       -0.3232
+     23  H         66.4190   87.5270   34.5040 H       1  LIG1        0.1686
+     24  C         64.6770   88.6690   34.2330 C.ar    1  LIG1        0.1601
+     25  N         64.1890   89.2810   33.1430 N.ar    1  LIG1       -0.1318
+     26  N         64.9640   89.0070   32.1450 N.ar    1  LIG1       -0.1293
+     27  F         69.9260   86.0280   29.3520 F       1  LIG1       -0.2042
+     28  C         68.9880   86.5420   30.0990 C.ar    1  LIG1        0.1401
+     29  C         67.6590   86.0900   29.9830 C.ar    1  LIG1        0.0297
+     30  C         66.6500   86.6450   30.7950 C.ar    1  LIG1        0.0053
+     31  C         66.9590   87.6470   31.7450 C.ar    1  LIG1        0.0359
+     32  C         68.2970   88.0990   31.8400 C.ar    1  LIG1        0.0053
+     33  C         69.3030   87.5560   31.0230 C.ar    1  LIG1        0.0297
+     34  C         66.9850   79.4910   34.8440 C.3     1  LIG1        0.4541
+     35  F         67.3150   78.4110   34.0640 F       1  LIG1       -0.1631
+     36  F         66.2460   80.3690   34.0910 F       1  LIG1       -0.1631
+     37  F         66.1920   79.0650   35.8800 F       1  LIG1       -0.1631
+@<TRIPOS>BOND
+     1     1     2    1
+     2     1    18    1
+     3     1    15    1
+     4     2     3    1
+     5     3     4    1
+     6     4     5    1
+     7     4    14    1
+     8     5    13   ar
+     9     5     6   ar
+    10     6     7   ar
+    11     7     8   ar
+    12     8     9   ar
+    13     8    12   ar
+    14     9    10   ar
+    15    10    11   ar
+    16    11    34    1
+    17    11    12   ar
+    18    12    13   ar
+    19    14    15    1
+    20    16    20    1
+    21    16    17    1
+    22    16    18   am
+    23    18    19    2
+    24    20    24    1
+    25    21    31    1
+    26    21    26   ar
+    27    21    22   ar
+    28    22    24   ar
+    29    22    23    1
+    30    24    25   ar
+    31    25    26   ar
+    32    27    28    1
+    33    28    29   ar
+    34    28    33   ar
+    35    29    30   ar
+    36    30    31   ar
+    37    31    32   ar
+    38    32    33   ar
+    39    34    35    1
+    40    34    36    1
+    41    34    37    1

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": [
+   {
+    "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",
+                "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"
+    }
+]

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "1.3.0",
+  "version": "4.3.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -13,11 +13,14 @@
   "scripts": {
     "lint": "eslint .",
     "lint-fix": "eslint . --fix",
-    "test": "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",
+    "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-extra": "cpx \"src/**/*.{scss,html,ico,jpg}\" 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\"",
@@ -25,17 +28,17 @@
     "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 --display minimal",
-    "watch-webpack-viewer": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.js",
-    "watch-webpack-viewer-debug": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.debug.js",
+    "watch-extra": "cpx \"src/**/*.{scss,html,ico,jpg}\" 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",
     "serve": "http-server -p 1338 -g",
     "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/${id}.mdb' --defaultPort 1336",
     "plugin-state": "node lib/commonjs/servers/plugin-state/index.js --working-folder ./build/state --port 1339",
     "preversion": "npm run test",
-    "version": "npm run build",
+    "version": "npm run rebuild && cpx .npmignore lib/",
     "postversion": "git push && git push --tags"
   },
   "files": [
@@ -45,6 +48,9 @@
   "bin": {
     "cif2bcif": "lib/commonjs/cli/cif2bcif/index.js",
     "cifschema": "lib/commonjs/cli/cifschema/index.js",
+    "mvs-validate": "lib/commonjs/cli/mvs/mvs-validate.js",
+    "mvs-render": "lib/commonjs/cli/mvs/mvs-render.js",
+    "mvs-print-schema": "lib/commonjs/cli/mvs/mvs-print-schema.js",
     "model-server": "lib/commonjs/servers/model/server.js",
     "model-server-query": "lib/commonjs/servers/model/query.js",
     "model-server-preprocess": "lib/commonjs/servers/model/preprocess.js",
@@ -72,7 +78,9 @@
       "node_modules",
       "lib"
     ],
-    "testURL": "http://localhost/",
+    "testEnvironmentOptions": {
+      "url": "http://localhost/"
+    },
     "testRegex": "\\.spec\\.ts$"
   },
   "author": "Mol* Contributors",
@@ -83,69 +91,106 @@
     "Áron Samuel Kovács <aron.kovacs@mail.muni.cz>",
     "Ludovic Autin <autin@scripps.edu>",
     "Michal Malý <michal.maly@ibt.cas.cz>",
-    "Jiří Černý <jiri.cerny@ibt.cas.cz>"
+    "Jiří Černý <jiri.cerny@ibt.cas.cz>",
+    "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>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^2.0.2",
-    "@graphql-codegen/cli": "^1.19.4",
-    "@graphql-codegen/time": "^2.0.2",
-    "@graphql-codegen/typescript": "^1.19.0",
-    "@graphql-codegen/typescript-graphql-files-modules": "^1.18.1",
-    "@graphql-codegen/typescript-graphql-request": "^2.0.3",
-    "@graphql-codegen/typescript-operations": "^1.17.12",
-    "@types/cors": "^2.8.8",
-    "@typescript-eslint/eslint-plugin": "^4.9.1",
-    "@typescript-eslint/parser": "^4.9.1",
+    "@types/cors": "^2.8.17",
+    "@types/gl": "^6.0.5",
+    "@types/pngjs": "^6.0.5",
+    "@types/jest": "^29.5.12",
+    "@types/react": "^18.3.1",
+    "@types/react-dom": "^18.3.0",
+    "@typescript-eslint/eslint-plugin": "^7.8.0",
+    "@typescript-eslint/parser": "^7.8.0",
     "benchmark": "^2.1.4",
-    "concurrently": "^5.3.0",
-    "cpx2": "^3.0.0",
-    "css-loader": "^5.0.1",
-    "eslint": "^7.15.0",
+    "concurrently": "^8.2.2",
+    "cpx2": "^7.0.1",
+    "crypto-browserify": "^3.12.0",
+    "css-loader": "^7.1.1",
+    "eslint": "^8.57.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
-    "fs-extra": "^9.0.1",
-    "graphql": "^15.4.0",
-    "http-server": "^0.12.3",
-    "jest": "^26.6.3",
-    "mini-css-extract-plugin": "^1.3.2",
-    "node-sass": "^5.0.0",
+    "fs-extra": "^11.2.0",
+    "http-server": "^14.1.1",
+    "jest": "^29.7.0",
+    "jpeg-js": "^0.4.4",
+    "mini-css-extract-plugin": "^2.9.0",
+    "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass-loader": "^10.1.0",
-    "simple-git": "^2.25.0",
-    "style-loader": "^2.0.0",
-    "ts-jest": "^26.4.4",
-    "typescript": "^4.1.2",
-    "webpack": "^4.44.1",
-    "webpack-cli": "^3.3.12",
-    "webpack-version-file-plugin": "^0.4.0"
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1",
+    "sass": "^1.76.0",
+    "sass-loader": "^14.2.1",
+    "simple-git": "^3.24.0",
+    "stream-browserify": "^3.0.0",
+    "style-loader": "^4.0.0",
+    "ts-jest": "^29.1.2",
+    "typescript": "^5.4.5",
+    "webpack": "^5.91.0",
+    "webpack-cli": "^5.1.4"
   },
   "dependencies": {
-    "@types/argparse": "^1.0.38",
-    "@types/benchmark": "^2.1.0",
-    "@types/compression": "1.7.0",
-    "@types/express": "^4.17.9",
-    "@types/jest": "^26.0.18",
-    "@types/node": "^14.14.11",
-    "@types/node-fetch": "^2.5.7",
-    "@types/react": "^17.0.0",
-    "@types/react-dom": "^17.0.0",
-    "@types/swagger-ui-dist": "3.30.0",
-    "argparse": "^1.0.10",
-    "body-parser": "^1.19.0",
+    "@types/argparse": "^2.0.16",
+    "@types/benchmark": "^2.1.5",
+    "@types/compression": "1.7.5",
+    "@types/express": "^4.17.21",
+    "@types/node": "^18.19.31",
+    "@types/node-fetch": "^2.6.11",
+    "@types/swagger-ui-dist": "3.30.4",
+    "argparse": "^2.0.1",
+    "body-parser": "^1.20.2",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
-    "express": "^4.17.1",
+    "express": "^4.19.2",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^8.0.0",
-    "immutable": "^3.8.2",
-    "node-fetch": "^2.6.1",
-    "react": "^17.0.1",
-    "react-dom": "^17.0.1",
-    "rxjs": "^6.6.3",
-    "swagger-ui-dist": "^3.37.2",
-    "tslib": "^2.0.3",
-    "util.promisify": "^1.0.1",
-    "xhr2": "^0.2.0"
+    "immer": "^10.1.1",
+    "immutable": "^4.3.5",
+    "io-ts": "^2.2.21",
+    "node-fetch": "^2.7.0",
+    "react-markdown": "^9.0.1",
+    "rxjs": "^7.8.1",
+    "swagger-ui-dist": "^5.17.2",
+    "tslib": "^2.6.2",
+    "util.promisify": "^1.1.2",
+    "xhr2": "^0.2.1"
+  },
+  "peerDependencies": {
+    "canvas": "^2.11.2",
+    "gl": "^6.0.2",
+    "jpeg-js": "^0.4.4",
+    "pngjs": "^6.0.0",
+    "react": "^18.1.0 || ^17.0.2 || ^16.14.0",
+    "react-dom": "^18.1.0 || ^17.0.2 || ^16.14.0"
+  },
+  "peerDependenciesMeta": {
+    "canvas": {
+      "optional": true
+    },
+    "gl": {
+      "optional": true
+    },
+    "jpeg-js": {
+      "optional": true
+    },
+    "pngjs": {
+      "optional": true
+    }
   }
 }

scripts/clean.js

@@ -0,0 +1,41 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <malym@ibt.cas.cz>
+ */
+
+const fs = require('fs');
+const path = require('path');
+
+function removeDir(dirPath) {
+    for (const ent of fs.readdirSync(dirPath)) {
+        const entryPath = path.join(dirPath, ent);
+        remove(entryPath);
+    }
+
+    fs.rmdirSync(dirPath);
+}
+
+function remove(entryPath) {
+    const st = fs.statSync(entryPath);
+    if (st.isDirectory())
+        removeDir(entryPath);
+    else
+        fs.unlinkSync(entryPath);
+}
+
+const toClean = [
+    path.resolve(__dirname, '../build'),
+    path.resolve(__dirname, '../lib'),
+    path.resolve(__dirname, '../tsconfig.tsbuildinfo'),
+];
+
+toClean.forEach(ph => {
+    if (fs.existsSync(ph)) {
+        try {
+            remove(ph);
+        } catch (err) {
+            console.warn(`Cleanup failed: ${err}`);
+        }
+    }
+});

scripts/deploy.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,6 +14,9 @@ const buildDir = path.resolve(__dirname, '../build/');
 const deployDir = path.resolve(buildDir, 'deploy/');
 const localPath = 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 --><iframe src="https://web3dsurvey.com/collector-iframe.html" style="width: 1px; height: 1px;"></iframe>`;
+
 function log(command, stdout, stderr) {
     if (command) {
         console.log('\n###', command);
@@ -22,11 +25,45 @@ function log(command, stdout, stderr) {
     }
 }
 
+function addAnalytics(path) {
+    const data = fs.readFileSync(path, 'utf8');
+    const result = data.replace(analyticsTag, analyticsCode);
+    fs.writeFileSync(path, result, 'utf8');
+}
+
 function copyViewer() {
     console.log('\n###', 'copy viewer files');
     const viewerBuildPath = path.resolve(buildDir, '../build/viewer/');
     const viewerDeployPath = path.resolve(localPath, 'viewer/');
     fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(viewerDeployPath, 'index.html'));
+}
+
+function copyMe() {
+    console.log('\n###', 'copy me files');
+    const meBuildPath = path.resolve(buildDir, '../build/mesoscale-explorer/');
+    const meDeployPath = path.resolve(localPath, 'me/');
+    fse.copySync(meBuildPath, meDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(meDeployPath, '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'));
+}
+
+function copyFiles() {
+    copyViewer();
+    copyMe();
+    copyDemos();
 }
 
 if (!fs.existsSync(localPath)) {
@@ -42,9 +79,9 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .outputHandler(log)
         .clone(remoteUrl, localPath)
         .fetch(['--all'])
-        .exec(copyViewer)
+        .exec(copyFiles)
         .add(['-A'])
-        .commit('updated viewer')
+        .commit('updated viewer & demos')
         .push();
 } else {
     console.log('\n###', 'update repository');
@@ -52,8 +89,8 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .outputHandler(log)
         .fetch(['--all'])
         .reset(['--hard', 'origin/master'])
-        .exec(copyViewer)
+        .exec(copyFiles)
         .add(['-A'])
-        .commit('updated viewer')
+        .commit('updated viewer & demos')
         .push();
 }

src/apps/docking-viewer/index.html

@@ -19,19 +19,19 @@
         <div id="app"></div>
         <script type="text/javascript" src="./molstar.js"></script>
         <script type="text/javascript">
-            var viewer = new DockingViewer('app', [0x33DD22, 0x1133EE], true);
-
             function getParam(name, regex) {
                 var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
                 return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
             }
-            var pdbqt = getParam('pdbqt', '[^&]+').trim();
-            var mol2 = getParam('mol2', '[^&]+').trim();
+            var pdbqt = getParam('pdbqt', '[^&]+').trim() || '../../examples/ace2.pdbqt';
+            var mol2 = getParam('mol2', '[^&]+').trim() || '../../examples/ace2-hit.mol2';
 
-            viewer.loadStructuresFromUrlsAndMerge([
-                { url: pdbqt, format: 'pdbqt' },
-                { url: mol2, format: 'mol2' }
-            ]);
+            DockingViewer.create('app', [0x33DD22, 0x1133EE], true).then(viewer => {
+                viewer.loadStructuresFromUrlsAndMerge([
+                    { url: pdbqt, format: 'pdbqt' },
+                    { url: mol2, format: 'mol2' }
+                ]);
+            });
         </script>
     </body>
 </html>

src/apps/docking-viewer/index.ts

@@ -5,30 +5,33 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import '../../mol-util/polyfill';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import './index.html';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { PluginConfig } from '../../mol-plugin/config';
-import { ObjectKeys } from '../../mol-util/type-helpers';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { Structure } from '../../mol-model/structure';
-import { PluginStateTransform, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Task } from '../../mol-task';
-import { StateObject } from '../../mol-state';
-import { ViewportComponent, StructurePreset, ShowButtons } from './viewport';
+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';
 import { PluginBehaviors } from '../../mol-plugin/behavior';
-import { ColorNames } from '../../mol-util/color/names';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { StateObject } from '../../mol-state';
+import { Task } from '../../mol-task';
 import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import './index.html';
+import { ShowButtons, StructurePreset, ViewportComponent } from './viewport';
 
 require('mol-plugin-ui/skin/light.scss');
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setProductionMode, setDebugMode } from '../../mol-util/debug';
+export { setDebugMode, setProductionMode } from '../../mol-util/debug';
+export { Viewer as DockingViewer };
 
 const DefaultViewerOptions = {
     extensions: ObjectKeys({}),
@@ -52,26 +55,30 @@ const DefaultViewerOptions = {
 };
 
 class Viewer {
-    plugin: PluginContext
+    constructor(public plugin: PluginUIContext) {
+    }
 
-    constructor(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,
+    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,
 
-            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: PluginSpec = {
-            actions: [...DefaultPluginSpec.actions],
+        const spec: PluginUISpec = {
+            actions: defaultSpec.actions,
             behaviors: [
                 PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci, { mark: false }),
                 PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
@@ -81,23 +88,23 @@ class Viewer {
                 PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
                 PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
             ],
-            animations: [...DefaultPluginSpec.animations || []],
-            customParamEditors: DefaultPluginSpec.customParamEditors,
+            animations: defaultSpec.animations,
+            customParamEditors: defaultSpec.customParamEditors,
             layout: {
                 initial: {
                     isExpanded: o.layoutIsExpanded,
                     showControls: o.layoutShowControls,
                     controlsDisplay: o.layoutControlsDisplay,
                 },
+            },
+            components: {
+                ...defaultSpec.components,
                 controls: {
-                    ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
+                    ...defaultSpec.components?.controls,
                     top: o.layoutShowSequence ? undefined : 'none',
                     bottom: o.layoutShowLog ? undefined : 'none',
                     left: o.layoutShowLeftPanel ? undefined : 'none',
-                }
-            },
-            components: {
-                ...DefaultPluginSpec.components,
+                },
                 remoteState: o.layoutShowRemoteState ? 'default' : 'none',
                 viewport: {
                     view: ViewportComponent
@@ -122,29 +129,29 @@ class Viewer {
             ? document.getElementById(elementOrId)
             : elementOrId;
         if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
-        this.plugin = createPlugin(element, spec);
+        const plugin = await createPluginUI({ target: element, spec, render: renderReact18 });
 
-        (this.plugin.customState as any) = {
+        (plugin.customState as any) = {
             colorPalette: {
                 name: 'colors',
                 params: { list: { colors } }
             }
         };
 
-        this.plugin.behaviors.canvas3d.initialized.subscribe(v => {
-            if (v) {
-                PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
-                    renderer: {
-                        ...this.plugin.canvas3d!.props.renderer,
-                        backgroundColor: ColorNames.white,
-                    },
-                    camera: {
-                        ...this.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: {} } }
+                }
             }
         });
+
+        return new Viewer(plugin);
     }
 
     async loadStructuresFromUrlsAndMerge(sources: { url: string, format: BuiltInTrajectoryFormat, isBinary?: boolean }[]) {
@@ -160,7 +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');
@@ -208,4 +215,3 @@ const MergeStructures = PluginStateTransform.BuiltIn({
 });
 
 (window as any).DockingViewer = Viewer;
-export { Viewer as DockingViewer };

src/apps/docking-viewer/viewport.tsx

@@ -1,38 +1,38 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import * as React from 'react';
-import { PluginUIComponent } from '../../mol-plugin-ui/base';
-import { Viewport, ViewportControls } from '../../mol-plugin-ui/viewport';
-import { BackgroundTaskProgress } from '../../mol-plugin-ui/task';
-import { LociLabels } from '../../mol-plugin-ui/controls';
-import { Toasts } from '../../mol-plugin-ui/toast';
-import { Button } from '../../mol-plugin-ui/controls/common';
-import { StructureRepresentationPresetProvider, presetStaticComponent } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { StateObjectRef } from '../../mol-state';
-import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { InteractionsRepresentationProvider } from '../../mol-model-props/computed/representations/interactions';
 import { InteractionTypeColorThemeProvider } from '../../mol-model-props/computed/themes/interaction-type';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginContext } from '../../mol-plugin/context';
+import { presetStaticComponent, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
 import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
-import { Color } from '../../mol-util/color';
+import { PluginUIComponent } from '../../mol-plugin-ui/base';
+import { LociLabels } from '../../mol-plugin-ui/controls';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { BackgroundTaskProgress } from '../../mol-plugin-ui/task';
+import { Toasts } from '../../mol-plugin-ui/toast';
+import { Viewport, ViewportControls } from '../../mol-plugin-ui/viewport';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginConfig } from '../../mol-plugin/config';
+import { PluginContext } from '../../mol-plugin/context';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { StateObjectRef } from '../../mol-state';
+import { Color } from '../../mol-util/color';
+import { Material } from '../../mol-util/material';
 
 function shinyStyle(plugin: PluginContext) {
     return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
         renderer: {
             ...plugin.canvas3d!.props.renderer,
-            style: { name: 'plastic', params: {} },
         },
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
             occlusion: { name: 'off', params: {} },
-            outline: { name: 'off', params: {} }
+            shadow: { name: 'off', params: {} },
+            outline: { name: 'off', params: {} },
         }
     } });
 }
@@ -41,20 +41,25 @@ function occlusionStyle(plugin: PluginContext) {
     return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
         renderer: {
             ...plugin.canvas3d!.props.renderer,
-            style: { name: 'flat', params: {} }
         },
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
             occlusion: { name: 'on', params: {
-                samples: 64,
-                radius: 8,
-                bias: 1.0,
-                blurKernelSize: 13
+                blurKernelSize: 15,
+                multiScale: { name: 'off', params: {} },
+                radius: 5,
+                bias: 0.8,
+                samples: 32,
+                resolutionScale: 1,
+                color: Color(0x000000),
             } },
             outline: { name: 'on', params: {
                 scale: 1.0,
-                threshold: 0.33
-            } }
+                threshold: 0.33,
+                color: Color(0x0000),
+                includeTransparent: true,
+            } },
+            shadow: { name: 'off', params: {} },
         }
     } });
 }
@@ -78,7 +83,7 @@ const PresetParams = {
     ...StructureRepresentationPresetProvider.CommonParams,
 };
 
-
+const CustomMaterial = Material({ roughness: 0.2, metalness: 0 });
 
 export const StructurePreset = StructureRepresentationPresetProvider({
     id: 'preset-structure',
@@ -95,8 +100,8 @@ export const StructurePreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.35 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams }, color: 'chain-id', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.35 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams, material: CustomMaterial }, color: 'chain-id', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -122,8 +127,8 @@ export const IllustrativePreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'spacefill', typeParams: { ...typeParams }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'spacefill', typeParams: { ...typeParams }, color: 'illustrative', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'spacefill', typeParams: { ...typeParams, ignoreLight: true }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'spacefill', typeParams: { ...typeParams, ignoreLight: true }, color: 'illustrative', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -150,8 +155,8 @@ const SurfacePreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: { ...typeParams, quality: 'custom', resolution: 0.5, doubleSided: true }, color: 'partial-charge' }, { tag: 'polymer' }),
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: { ...typeParams, material: CustomMaterial, quality: 'custom', resolution: 0.5, doubleSided: true }, color: 'partial-charge' }, { tag: 'polymer' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -178,8 +183,8 @@ const PocketPreset = StructureRepresentationPresetProvider({
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
-            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
-            surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: { ...typeParams, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }, color: 'partial-charge' }, { tag: 'surroundings' }),
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: { ...typeParams, material: CustomMaterial, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }, color: 'partial-charge' }, { tag: 'surroundings' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -202,15 +207,15 @@ 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, 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, 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 }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
-            label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
+            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, 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' }),
         };
 
         await update.commit({ revertOnError: true });
@@ -231,7 +236,7 @@ export class ViewportComponent extends PluginUIComponent {
 
     set = async (preset: StructureRepresentationPresetProvider) => {
         await this._set(this.plugin.managers.structure.hierarchy.selection.structures, preset);
-    }
+    };
 
     structurePreset = () => this.set(StructurePreset);
     illustrativePreset = () => this.set(IllustrativePreset);
@@ -239,7 +244,7 @@ export class ViewportComponent extends PluginUIComponent {
     pocketPreset = () => this.set(PocketPreset);
     interactionsPreset = () => this.set(InteractionsPreset);
 
-    get showButtons () {
+    get showButtons() {
         return this.plugin.config.get(ShowButtons);
     }
 

src/apps/mesoscale-explorer/app.ts

@@ -0,0 +1,280 @@
+/**
+ * Copyright (c) 2022-2023 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, loadPdbDev, 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';
+
+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,
+    stateRef?: string,
+    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,
+
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
+    viewportShowSelectionMode: false,
+    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
+};
+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);
+    }
+
+    async loadPdbDev(id: string) {
+        await loadPdbDev(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(MesoFocusLoci),
+                PluginSpec.Behavior(MesoSelectLoci),
+
+                ...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',
+            },
+            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.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();
+                } catch (e) {
+                    console.log(e);
+                }
+
+                (plugin.customState as MesoscaleExplorerState) = {
+                    examples,
+                    graphicsMode: o.graphicsMode,
+                    stateCache: {},
+                };
+
+                await MesoscaleState.init(plugin);
+            }
+        });
+
+        plugin.canvas3d?.setProps({
+            renderer: {
+                backgroundColor: Color(0x101010),
+            },
+            cameraFog: { name: 'off', params: {} },
+            hiZ: { enabled: true },
+        });
+
+        plugin.representation.structure.registry.clear();
+        plugin.representation.structure.registry.add(SpacefillRepresentationProvider);
+
+        plugin.state.setSnapshotParams({
+            image: true,
+            componentManager: false,
+            structureSelection: true,
+            behavior: 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 +1,75 @@
+/**
+ * Copyright (c) 2023 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';
+
+const B = ButtonsType;
+const M = ModifiersKeys;
+const Trigger = Binding.Trigger;
+
+const DefaultMesoFocusLociBindings = {
+    clickCenter: Binding([
+        Trigger(B.Flag.Primary, M.create()),
+    ], 'Camera center', 'Click element using ${triggers}'),
+    clickCenterFocus: Binding([
+        Trigger(B.Flag.Secondary, M.create()),
+    ], 'Camera center and focus', 'Click element using ${triggers}'),
+};
+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 } = this.params;
+                const radius = Math.max(sphere.radius + extraRadius, minRadius);
+
+                if (Binding.match(clickCenter, button, modifiers)) {
+                    if (Loci.isEmpty(current.loci)) {
+                        PluginCommands.Camera.Reset(this.ctx, { });
+                        return;
+                    }
+
+                    const snapshot = canvas3d.camera.getCenter(sphere.center);
+                    canvas3d.requestCameraReset({ durationMs, snapshot });
+                } else if (Binding.match(clickCenterFocus, button, modifiers)) {
+                    if (Loci.isEmpty(current.loci)) {
+                        PluginCommands.Camera.Reset(this.ctx, { });
+                        return;
+                    }
+
+                    const snapshot = canvas3d.camera.getCenter(sphere.center, radius);
+                    canvas3d.requestCameraReset({ durationMs, snapshot });
+                }
+            });
+        }
+    },
+    params: () => MesoFocusLociParams,
+    display: { name: 'Camera Meso Focus Loci on Canvas' }
+});

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

@@ -0,0 +1,164 @@
+/**
+ * Copyright (c) 2023 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';
+
+const B = ButtonsType;
+const M = ModifiersKeys;
+const Trigger = Binding.Trigger;
+
+const DefaultMesoSelectLociBindings = {
+    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 { 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' : 'chain');
+                    this.ctx.managers.interactivity.lociSelects.toggle({ loci }, false);
+                }
+            });
+            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 (modifiers.control) {
+                        this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EveryLoci }, false);
+                    } else {
+                        const loci = Loci.normalize(current.loci, 'chain');
+                        this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci }, false);
+                    }
+                }
+
+                if (Loci.isEmpty(current.loci)) {
+                    this.ctx.behaviors.labels.highlight.next({ labels: [] });
+                } else {
+                    const labels: string[] = [];
+                    if (StructureElement.Loci.is(current.loci)) {
+                        const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
+                        labels.push(cell?.obj?.label || 'Unknown');
+                    }
+                    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 +1,178 @@
+/**
+ * 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) || [];
+            // if (!unitsByEntity.get(idx)) {
+            //     console.log(entities.data.pdbx_description.value(idx));
+            // }
+            const structure = Structure.create(units);
+
+            const description = entities.data.pdbx_description.value(idx)[0] || 'model';
+            const label = description.split('.').at(-1) || a.label;
+
+            return new PSO.Molecule.Structure(structure, { label, description: `${a.description}` });
+        });
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});

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

@@ -0,0 +1,227 @@
+/**
+ * Copyright (c) 2019-2024 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'],
+            },
+        },
+        colorTheme: {
+            name: 'uniform',
+            params: {
+                value: color,
+                saturation: 0,
+                lightness: 0,
+            }
+        },
+        sizeTheme: {
+            name: 'physical',
+            params: {
+                value: 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()
+        .applyOrUpdateTagged('group:comp:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `comp:`, label: 'compartment', color: { type: 'custom', 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()
+        .applyOrUpdateTagged('group:func:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `func:`, label: 'function', color: { type: 'custom', 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)
+                        .applyOrUpdateTagged(`group:comp:${n}`, MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `comp:${p}`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                        .commit({ revertOnError: true });
+                    compGroups.set(n, group);
+                }
+            }
+
+            const f = entities.details.value(i) || 'unknown function';
+            if (!funcGroups.has(f)) {
+                const colorIdx = funcIds.get(f)?.idx;
+                const color = colorIdx !== undefined ? baseFuncColors[colorIdx] : ColorNames.white;
+                const group = await state.build()
+                    .to(funcRoot)
+                    .applyOrUpdateTagged(`group:func:${f}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'func:', state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                    .commit({ revertOnError: true });
+                funcGroups.set(f, group);
+            }
+        }
+
+        //
+
+        await state.transaction(async () => {
+            try {
+                const dependsOn = [base.ref];
+                plugin.animationLoop.stop({ noDraw: true });
+                let build: StateBuilder.Root | StateBuilder.To<any> = state.build();
+                for (let i = 0; i < entities._rowCount; i++) {
+                    const description = entities.pdbx_description.value(i)[0] || 'model';
+                    const d = description.split('.');
+                    const n = d.slice(0, -1).join('.');
+                    const l = d.at(-1)!;
+
+                    const f = entities.details.value(i) || 'unknown function';
+
+                    const color = compColors.get(n)![compIds.get(n)!.members.get(l)!];
+                    const sizeFactor = getSizeFactor(l);
+
+                    build = build
+                        .toRoot()
+                        .apply(CellpackStructure, { structureRef: base.ref, entityId: entities.id.value(i) }, { dependsOn })
+                        .apply(StructureRepresentation3D, getSpacefillParams(color, sizeFactor, graphicsMode), { tags: [`comp:${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 +1,139 @@
+/**
+ * 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('')),
+        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: 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 +1,581 @@
+/**
+ * Copyright (c) 2023-2024 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, updateColors } 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,
+            },
+        },
+        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, color: { type: 'custom', 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, color: { type: 'custom', 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 = ColorNames.skyblue;
+                const label = ent.label || ent.file.split('.')[0];
+                const sizeFactor = ent.sizeFactor || 1;
+                const tags = ent.groups.map(({ id, root }) => `${root}:${id}`);
+                const instances = ent.instances && getAssetInstances(ent.instances);
+
+                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 })
+                        .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();
+
+            const rootId = `${manifest.roots[0].id}:`;
+            const values = { type: 'group-generate', value: ColorNames.white, lightness: 0, alpha: 1 };
+            await updateColors(plugin, values, rootId, '');
+        } catch (e) {
+            console.error(e);
+            plugin.log.error(e);
+        } finally {
+            plugin.animationLoop.start();
+        }
+    }).run();
+
+    asset.dispose();
+}
+
+//
+
+type GenericRoot = {
+    id: string
+    label?: string
+    description?: string
+    children: GenericGroup[]
+}
+
+type GenericGroup = {
+    id: string
+    /** reference to `${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
+    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 +1,202 @@
+/**
+ * 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);
+            }
+
+            const label = entities.data.pdbx_description.value(idx).join(', ') || 'model';
+            return new PSO.Molecule.Structure(structure, { label, description: `${a.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 +1,182 @@
+/**
+ * Copyright (c) 2023-2024 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 { 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,
+            },
+        },
+        colorTheme: {
+            name: 'uniform',
+            params: {
+                value: color,
+                saturation: 0,
+                lightness: 0,
+            }
+        },
+        sizeTheme: {
+            name: 'physical',
+            params: {
+                value: 1,
+            }
+        },
+    };
+}
+
+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 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()
+        .applyOrUpdateTagged('group:ent:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'custom', 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:${t}`, label: t, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                .commit({ revertOnError: true });
+            entGroups.set(t, group);
+        }
+    }
+
+    //
+
+    await state.transaction(async () => {
+        try {
+            const dependsOn = [base.ref];
+            plugin.animationLoop.stop({ noDraw: true });
+            let build: StateBuilder.Root | StateBuilder.To<any> = state.build();
+            for (let i = 0; i < entities._rowCount; i++) {
+                const t = getEntityType(i);
+                const color = entColors.get(t)![entIds.get(t)!.members.get(i)!];
+                const scaleFactor = spheresAvgRadius.get(entities.id.value(i)) || 1;
+
+                build = build
+                    .toRoot()
+                    .apply(MmcifStructure, { structureRef: base.ref, entityId: entities.id.value(i) }, { dependsOn })
+                    .apply(StructureRepresentation3D, getSpacefillParams(color, scaleFactor, graphicsMode, clipVariant), { tags: [`ent:${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 +1,138 @@
+/**
+ * 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 label = pdbx_model.str(params.modelIndex);
+            const props = { label, description: Structure.elementDescription(s) };
+            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 +1,134 @@
+/**
+ * Copyright (c) 2022-2024 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,
+            },
+        },
+        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()
+        .applyOrUpdateTagged('group:ent:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', 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)
+        .applyOrUpdateTagged(`group:ent:mem`, MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', value: ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, 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`] });
+            }
+            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();
+}

src/apps/mesoscale-explorer/data/state.ts

@@ -0,0 +1,605 @@
+/**
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginStateObject as PSO, PluginStateTransform } from '../../../mol-plugin-state/objects';
+import { PluginContext } from '../../../mol-plugin/context';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Task } from '../../../mol-task';
+import { Color } from '../../../mol-util/color';
+import { Spheres } from '../../../mol-geo/geometry/spheres/spheres';
+import { Clip } from '../../../mol-util/clip';
+import { escapeRegExp, stringToWords } from '../../../mol-util/string';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { ParamMapping } from '../../../mol-util/param-mapping';
+import { EntityNode } from '../ui/entities';
+import { DistinctColorsProps, distinctColors } from '../../../mol-util/color/distinct';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { Hcl } from '../../../mol-util/color/spaces/hcl';
+import { StateObjectCell, StateObjectRef, StateSelection } from '../../../mol-state';
+import { ShapeRepresentation3D, StructureRepresentation3D } from '../../../mol-plugin-state/transforms/representation';
+import { SpacefillRepresentationProvider } from '../../../mol-repr/structure/representation/spacefill';
+import { assertUnreachable } from '../../../mol-util/type-helpers';
+import { MesoscaleExplorerState } from '../app';
+import { saturate } from '../../../mol-math/interpolate';
+
+function getHueRange(hue: number, variability: number) {
+    let min = hue - variability;
+    const minOverflow = (min < 0 ? -min : 0);
+    let max = hue + variability;
+    if (max > 360) min -= max - 360;
+    max += minOverflow;
+    return [Math.max(0, min), Math.min(360, max)] as [number, number];
+}
+
+function getGrayscaleColors(count: number, luminance: number, variability: number) {
+    const out: Color[] = [];
+    for (let i = 0; i < count; ++ i) {
+        const l = saturate(luminance / 100);
+        const v = saturate(variability / 180) * Math.random();
+        const s = Math.random() > 0.5 ? 1 : -1;
+        const d = Math.abs(l + s * v) % 1;
+        out[i] = Color.fromNormalizedRgb(d, d, d);
+    }
+    return out;
+}
+
+export function getDistinctGroupColors(count: number, color: Color, variability: number, shift: number, props?: Partial<DistinctColorsProps>) {
+    const hcl = Hcl.fromColor(Hcl(), color);
+    if (isNaN(hcl[0])) {
+        return getGrayscaleColors(count, hcl[2], variability);
+    }
+
+    if (count === 1) {
+        hcl[1] = 65;
+        hcl[2] = 55;
+        return [Hcl.toColor(hcl)];
+    }
+
+    const colors = distinctColors(count, {
+        hue: getHueRange(hcl[0], variability),
+        chroma: [30, 100],
+        luminance: [50, 100],
+        clusteringStepCount: 0,
+        minSampleCount: 1000,
+        sampleCountFactor: 100,
+        sort: 'none',
+        ...props,
+    });
+
+    if (shift !== 0) {
+        const offset = Math.floor(shift / 100 * count);
+        return [...colors.slice(offset), ...colors.slice(0, offset)];
+    } else {
+        return colors;
+    }
+}
+
+const Colors = [0x377eb8, 0xe41a1c, 0x4daf4a, 0x984ea3, 0xff7f00, 0xffff33, 0xa65628, 0xf781bf] as Color[];
+
+export function getDistinctBaseColors(count: number, shift: number, props?: Partial<DistinctColorsProps>): Color[] {
+    let colors: Color[];
+    if (count <= Colors.length) {
+        colors = Colors.slice(0, count).map(e => Array.isArray(e) ? e[0] : e);
+    } else {
+        colors = distinctColors(count, {
+            hue: [1, 360],
+            chroma: [25, 100],
+            luminance: [30, 100],
+            clusteringStepCount: 0,
+            minSampleCount: 1000,
+            sampleCountFactor: 100,
+            sort: 'none',
+            ...props,
+        });
+    }
+
+    if (shift !== 0) {
+        const offset = Math.floor(shift / 100 * count);
+        return [...colors.slice(offset), ...colors.slice(0, offset)];
+    } else {
+        return colors;
+    }
+}
+
+export const ColorParams = {
+    type: PD.Select('generate', PD.arrayToOptions(['generate', 'uniform', 'custom'])),
+    value: PD.Color(Color(0xFFFFFF), { hideIf: p => p.type === 'custom' }),
+    variability: PD.Numeric(20, { min: 1, max: 180, step: 1 }, { hideIf: p => p.type !== 'generate' }),
+    shift: PD.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }, { hideIf: p => p.type === 'custom' }),
+    alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
+    emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
+};
+export type ColorProps = PD.Values<typeof ColorParams>
+
+export const ColorValueParam = PD.Color(Color(0xFFFFFF));
+
+export const RootParams = {
+    type: PD.Select('custom', PD.arrayToOptions(['group-generate', 'group-uniform', 'generate', 'uniform', 'custom'])),
+    value: PD.Color(Color(0xFFFFFF), { hideIf: p => p.type !== 'uniform' }),
+    variability: PD.Numeric(20, { min: 1, max: 180, step: 1 }, { hideIf: p => p.type !== 'group-generate' }),
+    shift: PD.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }, { hideIf: p => p.type === 'custom' }),
+    alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
+    emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }, { hideIf: p => p.type === 'custom' }),
+};
+
+export const LightnessParams = {
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
+};
+export const DimLightness = 6;
+
+export const OpacityParams = {
+    alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+};
+
+export const EmissiveParams = {
+    emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }),
+};
+
+export const PatternParams = {
+    frequency: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+    amplitude: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+};
+
+export const LodParams = {
+    lodLevels: Spheres.Params.lodLevels,
+    cellSize: Spheres.Params.cellSize,
+    batchSize: Spheres.Params.batchSize,
+    approximate: Spheres.Params.approximate,
+};
+
+export const SimpleClipParams = {
+    type: PD.Select('none', PD.objectToOptions(Clip.Type, t => stringToWords(t))),
+    invert: PD.Boolean(false),
+    position: PD.Group({
+        x: PD.Numeric(0, { min: -100, max: 100, step: 1 }, { immediateUpdate: true }),
+        y: PD.Numeric(0, { min: -100, max: 100, step: 1 }, { immediateUpdate: true }),
+        z: PD.Numeric(0, { min: -100, max: 100, step: 1 }, { immediateUpdate: true }),
+    }, { hideIf: g => g.type === 'none', isExpanded: true }),
+    rotation: PD.Group({
+        axis: PD.Vec3(Vec3.create(1, 0, 0)),
+        angle: PD.Numeric(0, { min: -180, max: 180, step: 1 }, { immediateUpdate: true }),
+    }, { hideIf: g => g.type === 'none', isExpanded: true }),
+    scale: PD.Group({
+        x: PD.Numeric(100, { min: 0, max: 100, step: 1 }, { immediateUpdate: true }),
+        y: PD.Numeric(100, { min: 0, max: 100, step: 1 }, { immediateUpdate: true }),
+        z: PD.Numeric(100, { min: 0, max: 100, step: 1 }, { immediateUpdate: true }),
+    }, { hideIf: g => ['none', 'plane'].includes(g.type), isExpanded: true }),
+};
+export type SimpleClipParams = typeof SimpleClipParams
+export type SimpleClipProps = PD.Values<SimpleClipParams>
+
+export function getClipObjects(values: SimpleClipProps, boundingSphere: Sphere3D): Clip.Props['objects'] {
+    const { center, radius } = boundingSphere;
+
+    const position = Vec3.clone(center);
+    Vec3.add(position, position, Vec3.create(
+        radius * values.position.x / 100,
+        radius * values.position.y / 100,
+        radius * values.position.z / 100
+    ));
+
+    const scale = Vec3.create(values.scale.x, values.scale.y, values.scale.z);
+    Vec3.scale(scale, scale, 2 * radius / 100);
+
+    return [{
+        type: values.type,
+        invert: values.invert,
+        position,
+        scale,
+        rotation: values.rotation
+    }];
+}
+
+export function createClipMapping(node: EntityNode) {
+    return ParamMapping({
+        params: SimpleClipParams,
+        target: (ctx: PluginContext) => {
+            return node.clipValue;
+        }
+    })({
+        values(props, ctx) {
+            if (!props || props.objects.length === 0) {
+                return {
+                    type: 'none',
+                    invert: false,
+                    position: { x: 0, y: 0, z: 0 },
+                    rotation: { axis: Vec3.create(1, 0, 0), angle: 0 },
+                    scale: { x: 100, y: 100, z: 100 },
+                };
+            }
+
+            const { center, radius } = node.plugin.canvas3d!.boundingSphere;
+            const { invert, position, scale, rotation, type } = props.objects[0];
+
+            const p = Vec3.clone(position);
+            Vec3.sub(p, p, center);
+            Vec3.scale(p, p, 100 / radius);
+            Vec3.round(p, p);
+
+            const s = Vec3.clone(scale);
+            Vec3.scale(s, s, 100 / radius / 2);
+            Vec3.round(s, s);
+
+            return {
+                type,
+                invert,
+                position: { x: p[0], y: p[1], z: p[2] },
+                rotation,
+                scale: { x: s[0], y: s[1], z: s[2] },
+            };
+        },
+        update: (s, props) => {
+            if (!props) return;
+
+            const clipObjects = getClipObjects(s, node.plugin.canvas3d!.boundingSphere);
+            props.objects = clipObjects;
+        },
+        apply: async (props, ctx) => {
+            if (props) node.updateClip(props);
+        }
+    });
+}
+
+export const MesoscaleGroupParams = {
+    root: PD.Value<boolean>(false, { isHidden: true }),
+    index: PD.Value<number>(-1, { isHidden: true }),
+    tag: PD.Value<string>('', { isHidden: true }),
+    label: PD.Value<string>('', { isHidden: true }),
+    hidden: PD.Boolean(false),
+    color: PD.Group(RootParams),
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
+    alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+    emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }),
+    lod: PD.Group(LodParams),
+    clip: PD.Group(SimpleClipParams),
+};
+export type MesoscaleGroupProps = PD.Values<typeof MesoscaleGroupParams>;
+
+export class MesoscaleGroupObject extends PSO.Create({ name: 'Mesoscale Group', typeClass: 'Object' }) { }
+
+export const MesoscaleGroup = PluginStateTransform.BuiltIn({
+    name: 'mesoscale-group',
+    display: { name: 'Mesoscale Group' },
+    from: [PSO.Root, MesoscaleGroupObject],
+    to: MesoscaleGroupObject,
+    params: MesoscaleGroupParams,
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Apply Mesoscale Group', async () => {
+            return new MesoscaleGroupObject({}, { label: params.label });
+        });
+    },
+});
+
+export function getMesoscaleGroupParams(graphicsMode: GraphicsMode): MesoscaleGroupProps {
+    const groupParams = PD.getDefaultValues(MesoscaleGroupParams);
+    if (graphicsMode === 'custom') return groupParams;
+
+    return {
+        ...groupParams,
+        lod: {
+            ...groupParams.lod,
+            ...getGraphicsModeProps(graphicsMode),
+        }
+    };
+}
+
+//
+
+export type LodLevels = typeof SpacefillRepresentationProvider.defaultValues['lodLevels']
+
+export function getLodLevels(graphicsMode: Exclude<GraphicsMode, 'custom'>): LodLevels {
+    switch (graphicsMode) {
+        case 'performance':
+            return [
+                { minDistance: 1, maxDistance: 300, overlap: 0, stride: 1, scaleBias: 1 },
+                { minDistance: 300, maxDistance: 2000, overlap: 0, stride: 40, scaleBias: 3 },
+                { minDistance: 2000, maxDistance: 6000, overlap: 0, stride: 150, scaleBias: 3 },
+                { minDistance: 6000, maxDistance: 10000000, overlap: 0, stride: 300, scaleBias: 2.5 },
+            ];
+        case 'balanced':
+            return [
+                { minDistance: 1, maxDistance: 500, overlap: 0, stride: 1, scaleBias: 1 },
+                { minDistance: 500, maxDistance: 2000, overlap: 0, stride: 15, scaleBias: 3 },
+                { minDistance: 2000, maxDistance: 6000, overlap: 0, stride: 70, scaleBias: 2.7 },
+                { minDistance: 6000, maxDistance: 10000000, overlap: 0, stride: 200, scaleBias: 2.5 },
+            ];
+        case 'quality':
+            return [
+                { minDistance: 1, maxDistance: 1000, overlap: 0, stride: 1, scaleBias: 1 },
+                { minDistance: 1000, maxDistance: 4000, overlap: 0, stride: 10, scaleBias: 3 },
+                { minDistance: 4000, maxDistance: 10000, overlap: 0, stride: 50, scaleBias: 2.7 },
+                { minDistance: 10000, maxDistance: 10000000, overlap: 0, stride: 200, scaleBias: 2.3 },
+            ];
+        case 'ultra':
+            return [
+                { minDistance: 1, maxDistance: 2000, overlap: 0, stride: 1, scaleBias: 1 },
+                { minDistance: 2000, maxDistance: 8000, overlap: 0, stride: 10, scaleBias: 3 },
+                { minDistance: 8000, maxDistance: 20000, overlap: 0, stride: 50, scaleBias: 2.5 },
+                { minDistance: 20000, maxDistance: 10000000, overlap: 0, stride: 200, scaleBias: 2 },
+            ];
+        default:
+            assertUnreachable(graphicsMode);
+    }
+}
+
+export type GraphicsMode = 'ultra' | 'quality' | 'balanced' | 'performance' | 'custom';
+
+export function getGraphicsModeProps(graphicsMode: Exclude<GraphicsMode, 'custom'>) {
+    return {
+        lodLevels: getLodLevels(graphicsMode),
+        approximate: graphicsMode !== 'quality' && graphicsMode !== 'ultra',
+        alphaThickness: graphicsMode === 'performance' ? 15 : 12,
+    };
+}
+
+export function setGraphicsCanvas3DProps(ctx: PluginContext, graphics: GraphicsMode) {
+    const pixelScale = graphics === 'balanced' ? 0.75
+        : graphics === 'performance' ? 0.5 : 1;
+
+    ctx.canvas3dContext?.setProps({ pixelScale });
+
+    ctx.canvas3d?.setProps({
+        postprocessing: {
+            sharpening: pixelScale < 1 ? {
+                name: 'on',
+                params: { sharpness: 0.5, denoise: true }
+            } : { name: 'off', params: {} }
+        }
+    });
+}
+
+//
+
+export const MesoscaleStateParams = {
+    filter: PD.Value<string>('', { isHidden: true }),
+    graphics: PD.Select('quality', PD.arrayToOptions(['ultra', 'quality', 'balanced', 'performance', 'custom'] as GraphicsMode[])),
+    description: PD.Value<string>('', { isHidden: true }),
+    link: PD.Value<string>('', { isHidden: true }),
+};
+
+export class MesoscaleStateObject extends PSO.Create<MesoscaleState>({ name: 'Mesoscale State', typeClass: 'Object' }) { }
+
+const MesoscaleStateTransform = PluginStateTransform.BuiltIn({
+    name: 'mesoscale-state',
+    display: { name: 'Mesoscale State' },
+    from: PSO.Root,
+    to: MesoscaleStateObject,
+    params: MesoscaleStateParams,
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Apply Mesoscale State', async () => {
+            return new MesoscaleStateObject(params);
+        });
+    },
+});
+
+export { MesoscaleState };
+type MesoscaleState = PD.Values<typeof MesoscaleStateParams>;
+const MesoscaleState = {
+    async init(ctx: PluginContext) {
+        const cell = ctx.state.data.selectQ(q => q.ofType(MesoscaleStateObject))[0];
+        if (cell) throw new Error('MesoscaleState already initialized');
+
+        const customState = ctx.customState as MesoscaleExplorerState;
+        const state = await ctx.state.data.build().toRoot().apply(MesoscaleStateTransform, {
+            filter: '',
+            graphics: customState.graphicsMode,
+        }).commit();
+        customState.stateRef = state.ref;
+    },
+    get(ctx: PluginContext): MesoscaleState {
+        const ref = this.ref(ctx);
+        return ctx.state.data.tryGetCellData<MesoscaleStateObject>(ref);
+    },
+    async set(ctx: PluginContext, props: Partial<MesoscaleState>) {
+        const ref = this.ref(ctx);
+        await ctx.state.data.build().to(ref).update(MesoscaleStateTransform, old => Object.assign(old, props)).commit();
+    },
+    ref(ctx: PluginContext): string {
+        const ref = (ctx.customState as MesoscaleExplorerState).stateRef;
+        if (!ref) throw new Error('MesoscaleState not initialized');
+        return ref;
+    },
+    has(ctx: PluginContext): boolean {
+        const ref = (ctx.customState as MesoscaleExplorerState).stateRef || '';
+        return ctx.state.data.cells.has(ref) ? true : false;
+    },
+};
+
+//
+
+export function getRoots(plugin: PluginContext): StateSelection.CellSeq<StateObjectCell<MesoscaleGroupObject>> {
+    const s = plugin.customState as MesoscaleExplorerState;
+    if (!s.stateCache.roots) {
+        s.stateCache.roots = plugin.state.data.select(StateSelection.Generators.rootsOfType(MesoscaleGroupObject));
+    }
+    return s.stateCache.roots;
+}
+
+export function getGroups(plugin: PluginContext, tag?: string): StateSelection.CellSeq<StateObjectCell<MesoscaleGroupObject>> {
+    const s = plugin.customState as MesoscaleExplorerState;
+    const k = `groups-${tag || ''}`;
+    if (!s.stateCache[k]) {
+        const selector = tag !== undefined
+            ? StateSelection.Generators.ofTransformer(MesoscaleGroup).withTag(tag)
+            : StateSelection.Generators.ofTransformer(MesoscaleGroup);
+        s.stateCache[k] = plugin.state.data.select(selector);
+    }
+    return s.stateCache[k];
+}
+
+function _getAllGroups(plugin: PluginContext, tag: string | undefined, list: StateObjectCell[]) {
+    const groups = getGroups(plugin, tag);
+    list.push(...groups);
+    for (const g of groups) {
+        _getAllGroups(plugin, g.params?.values.tag, list);
+    }
+    return list;
+}
+
+export function getAllGroups(plugin: PluginContext, tag?: string) {
+    return _getAllGroups(plugin, tag, []);
+}
+
+export function getAllLeafGroups(plugin: PluginContext, tag: string) {
+    const allGroups = getAllGroups(plugin, tag);
+    allGroups.sort((a, b) => a.params?.values.index - b.params?.values.index);
+    return allGroups.filter(g => {
+        return getEntities(plugin, g.params?.values.tag).length > 0;
+    });
+}
+
+type EntityCells = StateSelection.CellSeq<StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D>>
+
+export function getEntities(plugin: PluginContext, tag?: string): EntityCells {
+    const s = plugin.customState as MesoscaleExplorerState;
+    const k = `entities-${tag || ''}`;
+    if (!s.stateCache[k]) {
+        const structureSelector = tag !== undefined
+            ? StateSelection.Generators.ofTransformer(StructureRepresentation3D).withTag(tag)
+            : StateSelection.Generators.ofTransformer(StructureRepresentation3D);
+        const shapeSelector = tag !== undefined
+            ? StateSelection.Generators.ofTransformer(ShapeRepresentation3D).withTag(tag)
+            : StateSelection.Generators.ofTransformer(ShapeRepresentation3D);
+        s.stateCache[k] = [
+            ...plugin.state.data.select(structureSelector).filter(c => c.obj!.data.sourceData.elementCount > 0),
+            ...plugin.state.data.select(shapeSelector),
+        ];
+    }
+    return s.stateCache[k];
+}
+
+function getFilterMatcher(filter: string) {
+    return filter.startsWith('"') && filter.endsWith('"')
+        ? new RegExp(`^${escapeRegExp(filter.substring(1, filter.length - 1))}$`, 'g')
+        : new RegExp(escapeRegExp(filter), 'gi');
+}
+
+export function getFilteredEntities(plugin: PluginContext, tag: string, filter: string) {
+    const matcher = getFilterMatcher(filter);
+    return getEntities(plugin, tag).filter(c => getEntityLabel(plugin, c).match(matcher) !== null);
+}
+
+function _getAllEntities(plugin: PluginContext, tag: string | undefined, list: EntityCells) {
+    list.push(...getEntities(plugin, tag));
+    for (const g of getGroups(plugin, tag)) {
+        _getAllEntities(plugin, g.params?.values.tag, list);
+    }
+    return list;
+}
+
+export function getAllEntities(plugin: PluginContext, tag?: string) {
+    return _getAllEntities(plugin, tag, []);
+}
+
+export function getAllFilteredEntities(plugin: PluginContext, tag: string, filter: string) {
+    const matcher = getFilterMatcher(filter);
+    return getAllEntities(plugin, tag).filter(c => getEntityLabel(plugin, c).match(matcher) !== null);
+}
+
+export function getEntityLabel(plugin: PluginContext, cell: StateObjectCell) {
+    return StateObjectRef.resolve(plugin.state.data, cell.transform.parent)?.obj?.label || 'Entity';
+}
+
+//
+
+export async function updateColors(plugin: PluginContext, values: PD.Values, tag: string, filter: string) {
+    const update = plugin.state.data.build();
+    const { type, value, shift, lightness, alpha, emissive } = values;
+
+    if (type === 'group-generate' || type === 'group-uniform') {
+        const groups = getAllLeafGroups(plugin, tag);
+        const baseColors = getDistinctBaseColors(groups.length, shift);
+
+        for (let i = 0; i < groups.length; ++i) {
+            const g = groups[i];
+            const entities = getFilteredEntities(plugin, g.params?.values.tag, filter);
+            let groupColors: Color[] = [];
+
+            if (type === 'group-generate') {
+                const c = g.params?.values.color;
+                groupColors = getDistinctGroupColors(entities.length, baseColors[i], c.variability, c.shift);
+            }
+
+            for (let j = 0; j < entities.length; ++j) {
+                const c = type === 'group-generate' ? groupColors[j] : baseColors[i];
+                update.to(entities[j]).update(old => {
+                    if (old.type) {
+                        old.colorTheme.params.value = c;
+                        old.colorTheme.params.lightness = lightness;
+                        old.type.params.alpha = alpha;
+                        old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
+                        old.type.params.emissive = emissive;
+                    } else if (old.coloring) {
+                        old.coloring.params.color = c;
+                        old.coloring.params.lightness = lightness;
+                        old.alpha = alpha;
+                        old.xrayShaded = alpha < 1 ? true : false;
+                        old.emissive = emissive;
+                    }
+                });
+            }
+
+            update.to(g.transform.ref).update(old => {
+                old.color.type = type === 'group-generate' ? 'generate' : 'uniform';
+                old.color.value = baseColors[i];
+                old.color.lightness = lightness;
+                old.color.alpha = alpha;
+                old.color.emissive = emissive;
+            });
+        }
+    } else if (type === 'generate' || type === 'uniform') {
+        const entities = getAllFilteredEntities(plugin, tag, filter);
+        let groupColors: Color[] = [];
+
+        if (type === 'generate') {
+            groupColors = getDistinctBaseColors(entities.length, shift);
+        }
+
+        for (let j = 0; j < entities.length; ++j) {
+            const c = type === 'generate' ? groupColors[j] : value;
+            update.to(entities[j]).update(old => {
+                if (old.type) {
+                    old.colorTheme.params.value = c;
+                    old.colorTheme.params.lightness = lightness;
+                    old.type.params.alpha = alpha;
+                    old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
+                    old.type.params.emissive = emissive;
+                } else if (old.coloring) {
+                    old.coloring.params.color = c;
+                    old.coloring.params.lightness = lightness;
+                    old.alpha = alpha;
+                    old.xrayShaded = alpha < 1 ? true : false;
+                    old.emissive = emissive;
+                }
+            });
+        }
+
+        const others = getAllLeafGroups(plugin, tag);
+        for (const o of others) {
+            update.to(o).update(old => {
+                old.color.type = type === 'generate' ? 'custom' : 'uniform';
+                old.color.value = value;
+                old.color.lightness = lightness;
+                old.color.alpha = alpha;
+                old.color.emissive = emissive;
+            });
+        }
+    }
+
+    await update.commit();
+};
+
+export function expandAllGroups(plugin: PluginContext) {
+    for (const g of getAllGroups(plugin)) {
+        if (g.state.isCollapsed) {
+            plugin.state.data.updateCellState(g.transform.ref, { isCollapsed: false });
+        }
+    }
+};

src/apps/mesoscale-explorer/data/util.ts

@@ -0,0 +1,87 @@
+/**
+ * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { OrderedSet, SortedArray } from '../../../mol-data/int';
+import { Box3D, GridLookup3D, PositionData, Sphere3D } from '../../../mol-math/geometry';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { ElementIndex, Unit } from '../../../mol-model/structure';
+
+export function mergeUnits(units: readonly Unit[], id: number): Unit {
+    const u = units[0];
+
+    let start = -1 as ElementIndex, end = -1 as ElementIndex;
+    let elements = SortedArray.Empty as SortedArray<ElementIndex>;
+
+    for (let i = 0, il = units.length; i < il; ++i) {
+        const e = units[i].elements;
+        if (SortedArray.isRange(e)) {
+            if (end !== -1 && e[0] === end + 1) {
+                // extend range
+                end = e[e.length - 1];
+            } else {
+                if (end !== -1) {
+                    // pending range
+                    elements = SortedArray.union(elements, SortedArray.ofRange(start, end));
+                }
+                // new range
+                start = e[0];
+                end = e[e.length - 1];
+            }
+        } else {
+            if (end !== -1) {
+                // pending range
+                elements = SortedArray.union(elements, SortedArray.ofRange(start, end));
+                start = -1 as ElementIndex, end = -1 as ElementIndex;
+            }
+            elements = SortedArray.union(elements, e);
+        }
+    }
+
+    if (end !== -1) {
+        // pending range
+        elements = SortedArray.union(elements, SortedArray.ofRange(start, end));
+    }
+
+    return Unit.create(id, id, 0, u.traits | Unit.Trait.MultiChain, u.kind, u.model, u.conformation.operator, elements);
+}
+
+export function partitionUnits(units: readonly Unit[], cellSize: number) {
+    const unitCount = units.length;
+    const mergedUnits: Unit[] = [];
+
+    const box = Box3D.setEmpty(Box3D());
+    const x = new Float32Array(unitCount);
+    const y = new Float32Array(unitCount);
+    const z = new Float32Array(unitCount);
+    const indices = OrderedSet.ofBounds(0, unitCount);
+
+    for (let i = 0, il = unitCount; i < il; ++i) {
+        const v = units[i].boundary.sphere.center;
+        x[i] = v[0];
+        y[i] = v[1];
+        z[i] = v[2];
+        Box3D.add(box, v);
+    }
+    Box3D.expand(box, box, Vec3.create(1, 1, 1));
+
+    const positionData: PositionData = { x, y, z, indices };
+    const boundary = { box, sphere: Sphere3D.fromBox3D(Sphere3D(), box) };
+    const lookup = GridLookup3D(positionData, boundary, Vec3.create(cellSize, cellSize, cellSize));
+
+    const { array, offset, count } = lookup.buckets;
+
+    for (let i = 0, il = offset.length; i < il; ++i) {
+        const start = offset[i];
+        const size = count[i];
+        const cellUnits: Unit[] = [];
+        for (let j = start, jl = start + size; j < jl; ++j) {
+            cellUnits.push(units[array[j]]);
+        }
+        mergedUnits.push(mergeUnits(cellUnits, i));
+    }
+
+    return mergedUnits;
+}

src/apps/mesoscale-explorer/index.html

@@ -0,0 +1,101 @@
+<!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">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Mol* Mesoscale Explorer</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+            }
+            html, body {
+                width: 100%;
+                height: 100%;
+                overflow: hidden;
+            }
+            hr {
+                margin: 10px;
+            }
+            h1, h2, h3, h4, h5 {
+                margin-top: 5px;
+                margin-bottom: 3px;
+            }
+            button {
+                padding: 2px;
+            }
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+
+            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
+            if (debugMode) molstar.setDebugMode(debugMode);
+
+            var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
+            if (timingMode) molstar.setTimingMode(timingMode);
+
+            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+            var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
+            var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
+            var graphicsMode = getParam('graphics-mode', '[^&]+').trim().toLowerCase();
+
+            molstar.MesoscaleExplorer.create('app', {
+                layoutShowControls: !hideControls,
+                viewportShowExpand: false,
+                preferWebgl1: preferWebgl1,
+                allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
+                powerPreference: powerPreference || 'high-performance',
+                graphicsMode: graphicsMode || 'quality',
+            }).then(me => {
+                var example = getParam('example', '[^&]+').trim();
+                if (example) {
+                    me.loadExample(example);
+                    return;
+                }
+
+                var url = getParam('url', '[^&]+').trim();
+                var type = getParam('type', '[^&]+').trim();
+                if (url && type) {
+                    me.loadUrl(url, type);
+                    return;
+                }
+
+                var pdb = getParam('pdb', '[^&]+').trim();
+                if (pdb) {
+                    me.loadPdb(pdb);
+                    return;
+                }
+
+                var pdbdev = getParam('pdbdev', '[^&]+').trim();
+                if (pdbdev) {
+                    me.loadPdbDev(pdbdev);
+                    return;
+                }
+
+                window.addEventListener('unload', () => {
+                    // to aid GC
+                    me.dispose();
+                });
+            });
+        </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
+    </body>
+</html>

src/apps/mesoscale-explorer/index.ts

@@ -0,0 +1,10 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import './favicon.ico';
+import './index.html';
+require('./style.scss');
+export * from './app';

src/apps/mesoscale-explorer/style.scss

@@ -0,0 +1,33 @@
+$default-background:         #2D3E50;
+$font-color:                 #EDF1F2;
+$hover-font-color:           #3B9AD9;
+$entity-current-font-color:  #FFFFFF;
+$msp-btn-remove-background:      #BF3A31;
+$msp-btn-remove-hover-font-color:#ffffff;
+$msp-btn-commit-on-font-color:   #ffffff;
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
+}
+
+@import 'mol-plugin-ui/skin/base/base';
+
+a {
+    color: $font-color;
+    &:hover {
+        color: $hover-font-color;
+    }
+}

src/apps/mesoscale-explorer/ui/entities.tsx

@@ -0,0 +1,973 @@
+/**
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginUIComponent } from '../../../mol-plugin-ui/base';
+import { Button, ControlGroup, IconButton } from '../../../mol-plugin-ui/controls/common';
+import { ArrowDropDownSvg, ArrowRightSvg, CloseSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg, ContentCutSvg, BrushSvg, SearchSvg } from '../../../mol-plugin-ui/controls/icons';
+import { PluginCommands } from '../../../mol-plugin/commands';
+import { State, StateObjectCell, StateSelection, StateTransformer } from '../../../mol-state';
+import { ParameterControls, ParameterMappingControl, ParamOnChange, SelectControl } from '../../../mol-plugin-ui/controls/parameters';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Clip } from '../../../mol-util/clip';
+import { StructureRepresentation3D } from '../../../mol-plugin-state/transforms/representation';
+import { Color } from '../../../mol-util/color';
+import { CombinedColorControl } from '../../../mol-plugin-ui/controls/color';
+import { MarkerAction } from '../../../mol-util/marker-action';
+import { EveryLoci, Loci } from '../../../mol-model/loci';
+import { deepEqual } from '../../../mol-util';
+import { ColorValueParam, ColorParams, ColorProps, DimLightness, LightnessParams, LodParams, MesoscaleGroup, MesoscaleGroupProps, OpacityParams, SimpleClipParams, SimpleClipProps, createClipMapping, getClipObjects, getDistinctGroupColors, RootParams, MesoscaleState, getRoots, getAllGroups, getAllLeafGroups, getFilteredEntities, getAllFilteredEntities, getGroups, getEntities, getAllEntities, getEntityLabel, updateColors, getGraphicsModeProps, GraphicsMode, MesoscaleStateParams, setGraphicsCanvas3DProps, PatternParams, expandAllGroups, EmissiveParams } from '../data/state';
+import React from 'react';
+import { MesoscaleExplorerState } from '../app';
+import { StructureElement } from '../../../mol-model/structure/structure/element';
+import { PluginStateObject as PSO } from '../../../mol-plugin-state/objects';
+import { Structure } from '../../../mol-model/structure';
+import { PluginContext } from '../../../mol-plugin/context';
+import { Sphere3D } from '../../../mol-math/geometry';
+
+function centerLoci(plugin: PluginContext, loci: Loci, durationMs = 250) {
+    const { canvas3d } = plugin;
+    if (!canvas3d) return;
+
+    const sphere = Loci.getBoundingSphere(loci) || Sphere3D();
+    const snapshot = canvas3d.camera.getCenter(sphere.center);
+    canvas3d.requestCameraReset({ durationMs, snapshot });
+}
+
+export class ModelInfo extends PluginUIComponent<{}, { isDisabled: boolean }> {
+    state = {
+        isDisabled: false,
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
+            this.setState({ isDisabled: v });
+        });
+
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (!this.state.isDisabled && MesoscaleState.has(this.plugin) && MesoscaleState.ref(this.plugin) === e.ref) {
+                this.forceUpdate();
+            }
+        });
+    }
+
+    get info() {
+        if (!MesoscaleState.has(this.plugin)) return;
+
+        const state = MesoscaleState.get(this.plugin);
+        if (!state.description && !state.link) return;
+
+        return {
+            description: state.description,
+            link: state.link,
+        };
+    }
+
+    render() {
+        const info = this.info;
+        return info && <>
+            <div className='msp-help-text'>
+                <div>{info.description}</div>
+                <div><a href={info.link} target='_blank'>Source</a></div>
+            </div>
+        </>;
+    }
+}
+
+const SelectionStyleParam = PD.Select('color+outline', PD.objectToOptions({
+    'color+outline': 'Color & Outline',
+    'color': 'Color',
+    'outline': 'Outline'
+} as const));
+type SelectionStyle = typeof SelectionStyleParam['defaultValue']
+
+export class SelectionInfo extends PluginUIComponent<{}, { isDisabled: boolean }> {
+    state = {
+        isDisabled: false,
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
+            this.setState({ isDisabled: v });
+        });
+
+        this.subscribe(this.plugin.managers.structure.selection.events.changed, e => {
+            if (!this.state.isDisabled) {
+                this.forceUpdate();
+            }
+        });
+    }
+
+    get info() {
+        const info: { label: string, key: string }[] = [];
+        this.plugin.managers.structure.selection.entries.forEach((e, k) => {
+            if (StructureElement.Loci.is(e.selection) && !StructureElement.Loci.isEmpty(e.selection)) {
+                const cell = this.plugin.helpers.substructureParent.get(e.selection.structure);
+                info.push({
+                    label: cell?.obj?.label || 'Unknown',
+                    key: k,
+                });
+            }
+        });
+        return info;
+    }
+
+    find(label: string) {
+        MesoscaleState.set(this.plugin, { filter: `"${label}"` });
+        if (label) expandAllGroups(this.plugin);
+    };
+
+    remove(key: string) {
+        const e = this.plugin.managers.structure.selection.entries.get(key);
+        if (!e) return;
+
+        const loci = Structure.toStructureElementLoci(e.selection.structure);
+        this.plugin.managers.interactivity.lociSelects.deselect({ loci }, false);
+    }
+
+    center(key: string) {
+        const e = this.plugin.managers.structure.selection.entries.get(key);
+        if (!e) return;
+
+        const loci = Structure.toStructureElementLoci(e.selection.structure);
+        centerLoci(this.plugin, loci);
+    }
+
+    get selection() {
+        const info = this.info;
+        if (!info.length) return <>
+            <div className='msp-help-text'>
+                <div>Use <i>ctrl+left click</i> to select entities, either on the 3D canvas or in the tree below</div>
+            </div>
+        </>;
+
+        return <>
+            {info.map((entry, index) => {
+                const label = <Button className={`msp-btn-tree-label`} noOverflow disabled={this.state.isDisabled}
+                    onClick={() => this.center(entry.key)}
+                >
+                    <span title={entry.label}>{entry.label}</span>
+                </Button>;
+                const find = <IconButton svg={SearchSvg} toggleState={false} disabled={this.state.isDisabled} small onClick={() => this.find(entry.label)} />;
+                const remove = <IconButton svg={CloseSvg} toggleState={false} disabled={this.state.isDisabled} onClick={() => this.remove(entry.key)} />;
+                return <div key={index} className={`msp-flex-row`} style={{ margin: `1px 5px 1px ${1 * 10 + 5}px` }}>
+                    {label}
+                    {find}
+                    {remove}
+                </div>;
+            })}
+        </>;
+    }
+
+    get style() {
+        const p = this.plugin.canvas3d?.props;
+        if (!p) return;
+
+        if (p.renderer.dimStrength === 1 && p.marking.enabled) return 'color+outline';
+        if (p.renderer.dimStrength === 1) return 'color';
+        if (p.marking.enabled) return 'outline';
+    }
+
+    setStyle(value: SelectionStyle) {
+        if (value.includes('color') && value.includes('outline')) {
+            this.plugin.canvas3d?.setProps({
+                renderer: {
+                    dimStrength: 1,
+                },
+                marking: {
+                    enabled: true
+                }
+            });
+        } else if (value.includes('color')) {
+            this.plugin.canvas3d?.setProps({
+                renderer: {
+                    dimStrength: 1,
+                },
+                marking: {
+                    enabled: false
+                }
+            });
+        } else if (value.includes('outline')) {
+            this.plugin.canvas3d?.setProps({
+                renderer: {
+                    dimStrength: 0,
+                    selectStrength: 0.3,
+                },
+                marking: {
+                    enabled: true
+                }
+            });
+        } else {
+            this.plugin.canvas3d?.setProps({
+                renderer: {
+                    dimStrength: 0,
+                    selectStrength: 0,
+                },
+                marking: {
+                    enabled: false
+                }
+            });
+        }
+
+        this.forceUpdate();
+    }
+
+    renderStyle() {
+        const style = this.style || '';
+        return <div style={{ margin: '5px', marginBottom: '10px' }}>
+            <SelectControl name={'Style'} param={SelectionStyleParam} value={style} onChange={(e) => { this.setStyle(e.value); }} />
+        </div>;
+    }
+
+    render() {
+        return <>
+            {this.renderStyle()}
+            {this.selection}
+        </>;
+    }
+}
+
+export class EntityControls extends PluginUIComponent<{}, { isDisabled: boolean }> {
+    filterRef = React.createRef<HTMLInputElement>();
+    prevFilter = '';
+    filterFocus = false;
+
+    state = {
+        isDisabled: false,
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.state.events.object.created, e => {
+            this.forceUpdate();
+        });
+
+        this.subscribe(this.plugin.state.events.object.removed, e => {
+            this.forceUpdate();
+        });
+
+        this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
+            this.setState({ isDisabled: v });
+        });
+
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (!this.state.isDisabled && this.roots.some(r => e.cell === r) || (MesoscaleState.has(this.plugin) && MesoscaleState.ref(this.plugin) === e.ref)) {
+                this.forceUpdate();
+            }
+        });
+    }
+
+    componentDidUpdate(): void {
+        const filter = this.filter;
+        if (this.filterFocus) {
+            this.filterRef.current?.focus();
+            this.prevFilter = filter;
+        }
+    }
+
+    get roots() {
+        return getRoots(this.plugin);
+    }
+
+    setGroupBy = (value: number) => {
+        this.roots.forEach((c, i) => {
+            if (c.state.isHidden && value === i || !c.state.isHidden && value !== i) {
+                PluginCommands.State.ToggleVisibility(this.plugin, { state: c.parent!, ref: c.transform.ref });
+            }
+        });
+    };
+
+    get groupBy() {
+        const roots = this.roots;
+        for (let i = 0, il = roots.length; i < il; ++i) {
+            if (!roots[i].state.isHidden) return i;
+        }
+        return 0;
+    }
+
+    setFilter = (value: string) => {
+        this.filterFocus = true;
+        const filter = value.trim().replace(/\s+/gi, ' ');
+        MesoscaleState.set(this.plugin, { filter });
+        if (filter) expandAllGroups(this.plugin);
+    };
+
+    get filter() {
+        return MesoscaleState.has(this.plugin) ? MesoscaleState.get(this.plugin).filter : '';
+    }
+
+    setGraphics = (graphics: GraphicsMode) => {
+        MesoscaleState.set(this.plugin, { graphics });
+        (this.plugin.customState as MesoscaleExplorerState).graphicsMode = graphics;
+
+        if (graphics === 'custom') return;
+
+        const update = this.plugin.state.data.build();
+
+        const { lodLevels, approximate, alphaThickness } = getGraphicsModeProps(graphics);
+
+        for (const r of getAllEntities(this.plugin)) {
+            update.to(r).update(old => {
+                if (old.type) {
+                    old.type.params.lodLevels = lodLevels;
+                    old.type.params.approximate = approximate;
+                    old.type.params.alphaThickness = alphaThickness;
+                }
+            });
+        }
+
+        for (const g of getAllGroups(this.plugin)) {
+            update.to(g).update(old => {
+                old.lod.lodLevels = lodLevels;
+                old.lod.approximate = approximate;
+            });
+        }
+
+        update.commit();
+
+        setGraphicsCanvas3DProps(this.plugin, graphics);
+    };
+
+    get graphics() {
+        const customState = this.plugin.customState as MesoscaleExplorerState;
+        return MesoscaleState.has(this.plugin) ? MesoscaleState.get(this.plugin).graphics : customState.graphicsMode;
+    }
+
+    renderGraphics() {
+        const graphics = this.graphics;
+        return <div style={{ margin: '5px', marginBottom: '10px' }}>
+            <SelectControl name={'Graphics'} param={MesoscaleStateParams.graphics} value={`${graphics}`} onChange={(e) => { this.setGraphics(e.value); }} />
+        </div>;
+    }
+
+    render() {
+        const roots = this.roots;
+        if (roots.length === 0 || !MesoscaleState.has(this.plugin)) {
+            return <>
+                {this.renderGraphics()}
+            </>;
+        }
+
+        const disabled = this.state.isDisabled;
+        const groupBy = this.groupBy;
+
+        const options: [string, string][] = [];
+        roots.forEach((c, i) => {
+            options.push([`${i}`, c.obj!.label]);
+        });
+        const groupParam = PD.Select(options[0][0], options);
+        const root = roots.length === 1 ? roots[0] : roots[groupBy];
+
+        const filter = this.filter;
+
+        return <>
+            {this.renderGraphics()}
+            <div className={`msp-flex-row msp-control-row`} style={{ margin: '5px', marginBottom: '10px' }}>
+                <input type='text' ref={this.filterRef}
+                    value={filter}
+                    placeholder='Search'
+                    onChange={e => this.setFilter(e.target.value)}
+                    disabled={disabled}
+                    onBlur={() => this.filterFocus = false}
+                />
+                <IconButton svg={CloseSvg} toggleState={false} disabled={disabled} onClick={() => this.setFilter('')} />
+            </div>
+            {options.length > 1 && <div style={{ margin: '5px', marginBottom: '10px' }}>
+                <SelectControl name={'Group By'} param={groupParam} value={`${groupBy}`} onChange={(e) => { this.setGroupBy(parseInt(e.value)); }} />
+            </div>}
+            <GroupNode filter={filter} cell={root} depth={0} />
+        </>;
+    }
+}
+
+class Node<P extends {}, S extends { isDisabled: boolean }> extends PluginUIComponent<P & { cell: StateObjectCell, depth: number }, S> {
+
+    is(e: State.ObjectEvent) {
+        return e.ref === this.ref && e.state === this.props.cell.parent;
+    }
+
+    get ref() {
+        return this.props.cell.transform.ref;
+    }
+
+    get cell() {
+        return this.props.cell;
+    }
+
+    get roots() {
+        return getRoots(this.plugin);
+    }
+
+    componentDidMount() {
+        this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
+            this.setState({ isDisabled: v });
+        });
+
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (!this.state.isDisabled && this.is(e)) {
+                this.forceUpdate();
+            }
+        });
+    }
+}
+
+export class GroupNode extends Node<{ filter: string }, { isCollapsed: boolean, action?: 'color' | 'clip' | 'root', isDisabled: boolean }> {
+    state = {
+        isCollapsed: !!this.props.cell.state.isCollapsed,
+        action: undefined,
+        isDisabled: false,
+    };
+
+    toggleExpanded = (e: React.MouseEvent<HTMLElement>) => {
+        PluginCommands.State.ToggleExpanded(this.plugin, { state: this.cell.parent!, ref: this.ref });
+    };
+
+    toggleColor = (e?: React.MouseEvent<HTMLButtonElement, MouseEvent>) => {
+        this.setState({ action: this.state.action === 'color' ? undefined : 'color' });
+    };
+
+    toggleClip = () => {
+        this.setState({ action: this.state.action === 'clip' ? undefined : 'clip' });
+    };
+
+    toggleRoot = () => {
+        this.setState({ action: this.state.action === 'root' ? undefined : 'root' });
+    };
+
+    highlight = (e: React.MouseEvent<HTMLElement>) => {
+        e.preventDefault();
+        this.plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+        for (const r of this.allFilteredEntities) {
+            const repr = r.obj?.data.repr;
+            if (repr) {
+                this.plugin.canvas3d?.mark({ repr, loci: EveryLoci }, MarkerAction.Highlight);
+            }
+        }
+    };
+
+    clearHighlight = (e: React.MouseEvent<HTMLElement>) => {
+        e.preventDefault();
+        this.plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+        e.currentTarget.blur();
+    };
+
+    get groups() {
+        return getGroups(this.plugin, this.cell.params?.values.tag);
+    }
+
+    get allGroups() {
+        const allGroups = getAllGroups(this.plugin, this.cell.params?.values.tag);
+        allGroups.push(this.cell);
+        return allGroups;
+    }
+
+    get entities() {
+        return getEntities(this.plugin, this.cell.params?.values.tag);
+    }
+
+    get filteredEntities() {
+        return getFilteredEntities(this.plugin, this.cell.params?.values.tag, this.props.filter);
+    }
+
+    get allEntities() {
+        return getAllEntities(this.plugin, this.cell.params?.values.tag);
+    }
+
+    get allFilteredEntities() {
+        return getAllFilteredEntities(this.plugin, this.cell.params?.values.tag, this.props.filter);
+    }
+
+    toggleVisible = (e: React.MouseEvent<HTMLElement>) => {
+        PluginCommands.State.ToggleVisibility(this.plugin, { state: this.cell.parent!, ref: this.ref });
+        const isHidden = this.cell.state.isHidden;
+
+        for (const r of this.allFilteredEntities) {
+            this.plugin.state.data.updateCellState(r.transform.ref, { isHidden });
+        }
+
+        this.plugin.build().to(this.ref).update(old => {
+            old.hidden = isHidden;
+        }).commit();
+    };
+
+    updateColor = (values: ColorProps) => {
+        const update = this.plugin.state.data.build();
+        const { value, type, lightness, alpha, emissive } = values;
+
+        const entities = this.filteredEntities;
+
+        let groupColors: Color[] = [];
+
+        if (type === 'generate') {
+            groupColors = getDistinctGroupColors(entities.length, value, values.variability, values.shift);
+        }
+
+        for (let i = 0; i < entities.length; ++i) {
+            const c = type === 'generate' ? groupColors[i] : value;
+            update.to(entities[i]).update(old => {
+                if (old.type) {
+                    old.colorTheme.params.value = c;
+                    old.colorTheme.params.lightness = lightness;
+                    old.type.params.alpha = alpha;
+                    old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
+                    old.type.params.emissive = emissive;
+                } else {
+                    old.coloring.params.color = c;
+                    old.coloring.params.lightness = lightness;
+                    old.alpha = alpha;
+                    old.xrayShaded = alpha < 1 ? true : false;
+                    old.emissive = emissive;
+                }
+            });
+        }
+
+        update.to(this.ref).update(old => {
+            old.color = values;
+        });
+
+        for (const r of this.roots) {
+            update.to(r).update(old => {
+                old.color.type = 'custom';
+            });
+        }
+
+        update.commit();
+    };
+
+    updateRoot = async (values: PD.Values) => {
+        await updateColors(this.plugin, values, this.cell.params?.values.tag, this.props.filter);
+
+        const update = this.plugin.state.data.build();
+
+        for (const r of this.roots) {
+            if (r !== this.cell) {
+                update.to(r).update(old => {
+                    old.color.type = 'custom';
+                });
+                const others = getAllLeafGroups(this.plugin, r.params?.values.tag);
+                for (const o of others) {
+                    update.to(o).update(old => {
+                        old.color.type = 'custom';
+                    });
+                }
+            }
+        }
+
+        update.to(this.ref).update(old => {
+            old.color = values;
+        });
+
+        update.commit();
+    };
+
+    updateClip = (values: PD.Values) => {
+        const update = this.plugin.state.data.build();
+        const clipObjects = getClipObjects(values as SimpleClipProps, this.plugin.canvas3d!.boundingSphere);
+
+        for (const r of this.allFilteredEntities) {
+            update.to(r).update(old => {
+                if (old.type) {
+                    old.type.params.clip.objects = clipObjects;
+                } else {
+                    old.clip.objects = clipObjects;
+                }
+            });
+        }
+
+        for (const g of this.allGroups) {
+            update.to(g).update(old => {
+                old.clip = values;
+            });
+        }
+
+        update.commit();
+    };
+
+    updateLod = (values: PD.Values) => {
+        MesoscaleState.set(this.plugin, { graphics: 'custom' });
+        (this.plugin.customState as MesoscaleExplorerState).graphicsMode = 'custom';
+
+        const update = this.plugin.state.data.build();
+
+        for (const r of this.allFilteredEntities) {
+            update.to(r).update(old => {
+                if (old.type) {
+                    old.type.params.lodLevels = values.lodLevels;
+                    old.type.params.cellSize = values.cellSize;
+                    old.type.params.batchSize = values.batchSize;
+                    old.type.params.approximate = values.approximate;
+                }
+            });
+        }
+
+        for (const g of this.allGroups) {
+            update.to(g).update(old => {
+                old.lod = values;
+            });
+        }
+
+        update.commit();
+    };
+
+    update = (props: MesoscaleGroupProps) => {
+        this.plugin.state.data.build().to(this.ref).update(props);
+    };
+
+    renderColor() {
+        const color = this.cell.params?.values.color;
+        if (this.cell.params?.values.color.type === 'uniform') {
+            const style = {
+                backgroundColor: Color.toStyle(color.value),
+                minWidth: 32,
+                width: 32,
+                borderRight: `6px solid ${Color.toStyle(Color.lighten(color.value, color.lightness))}`
+            };
+            return <Button style={style} onClick={this.toggleColor} />;
+        } else if (this.cell.params?.values.color.type === 'generate') {
+            const style = {
+                minWidth: 32,
+                width: 32,
+                borderRight: `6px solid ${Color.toStyle(Color.lighten(color.value, color.lightness))}`
+            };
+            return <IconButton style={style} svg={BrushSvg} toggleState={false} small onClick={this.toggleColor} />;
+        } else {
+            return <IconButton svg={BrushSvg} toggleState={false} small onClick={this.toggleColor} />;
+        }
+    }
+
+    render() {
+        if (this.allFilteredEntities.length === 0) return;
+
+        const state = this.cell.state;
+        const disabled = false;
+        const groupLabel = this.cell.obj!.label;
+        const depth = this.props.depth;
+        const colorValue = this.cell.params?.values.color;
+        const rootValue = this.cell.params?.values.color;
+        const clipValue = this.cell.params?.values.clip;
+        const lodValue = this.cell.params?.values.lod;
+        const isRoot = this.cell.params?.values.root;
+
+        const groups = this.groups;
+        const entities = this.entities;
+
+        const label = <Button className={`msp-btn-tree-label`} noOverflow disabled={disabled}
+            onMouseEnter={this.highlight}
+            onMouseLeave={this.clearHighlight}
+        >
+            <span title={groupLabel}>{groupLabel}</span>
+        </Button>;
+
+        const expand = <IconButton svg={state.isCollapsed ? ArrowRightSvg : ArrowDropDownSvg} flex='20px' disabled={disabled} onClick={this.toggleExpanded} transparent className='msp-no-hover-outline' style={{ visibility: groups.length > 0 || entities.length > 0 ? 'visible' : 'hidden' }} />;
+        const color = (entities.length > 0 && !isRoot) && this.renderColor();
+        const root = (isRoot && this.allGroups.length > 1) && <IconButton svg={BrushSvg} toggleState={false} disabled={disabled} small onClick={this.toggleRoot} />;
+        const clip = <IconButton svg={ContentCutSvg} toggleState={false} disabled={disabled} small onClick={this.toggleClip} />;
+        const visibility = <IconButton svg={state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg} toggleState={false} disabled={disabled} small onClick={this.toggleVisible} />;
+
+        return <>
+            <div className={`msp-flex-row`} style={{ margin: `1px 5px 1px ${depth * 10 + 5}px` }}>
+                {expand}
+                {label}
+                {root || color}
+                {clip}
+                {visibility}
+            </div>
+            {this.state.action === 'color' && <div style={{ marginRight: 5 }} className='msp-accent-offset'>
+                <ControlGroup header='Color' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleColor}
+                    topRightIcon={CloseSvg} noTopMargin childrenClassName='msp-viewport-controls-panel-controls'>
+                    <ParameterControls params={ColorParams} values={colorValue} onChangeValues={this.updateColor} />
+                </ControlGroup>
+            </div>}
+            {this.state.action === 'clip' && <div style={{ marginRight: 5 }} className='msp-accent-offset'>
+                <ControlGroup header='Clip' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleClip}
+                    topRightIcon={CloseSvg} noTopMargin childrenClassName='msp-viewport-controls-panel-controls'>
+                    <ParameterControls params={SimpleClipParams} values={clipValue} onChangeValues={this.updateClip} />
+                    <ParameterControls params={LodParams} values={lodValue} onChangeValues={this.updateLod} />
+                </ControlGroup>
+            </div>}
+            {this.state.action === 'root' && <div style={{ marginRight: 5 }} className='msp-accent-offset'>
+                <ControlGroup header='Color' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleRoot}
+                    topRightIcon={CloseSvg} noTopMargin childrenClassName='msp-viewport-controls-panel-controls'>
+                    <ParameterControls params={RootParams} values={rootValue} onChangeValues={this.updateRoot} />
+                </ControlGroup>
+            </div>}
+            {(!state.isCollapsed) && <>
+                {groups.map(c => {
+                    return <GroupNode filter={this.props.filter} cell={c} depth={depth + 1} key={c.transform.ref} />;
+                })}
+                {this.filteredEntities.map(c => {
+                    return <EntityNode cell={c} depth={depth + 1} key={c.transform.ref} />;
+                })}
+            </>}
+        </>;
+    }
+}
+
+export class EntityNode extends Node<{}, { action?: 'color' | 'clip', isDisabled: boolean }> {
+    state = {
+        action: undefined,
+        isDisabled: false,
+    };
+
+    clipMapping = createClipMapping(this);
+
+    get groups() {
+        return this.plugin.state.data.select(StateSelection.Generators.ofTransformer(MesoscaleGroup)
+            .filter(c => !!this.cell.transform.tags?.includes(c.params?.values.tag)));
+    }
+
+    toggleVisible = (e: React.MouseEvent<HTMLElement>) => {
+        e.preventDefault();
+        PluginCommands.State.ToggleVisibility(this.plugin, { state: this.props.cell.parent!, ref: this.ref });
+        e.currentTarget.blur();
+    };
+
+    toggleColor = (e?: React.MouseEvent<HTMLButtonElement, MouseEvent>) => {
+        if (e?.ctrlKey) {
+            this.updateLightness({ lightness: this.lightnessValue?.lightness ? 0 : DimLightness });
+            e.preventDefault();
+        } else {
+            this.setState({ action: this.state.action === 'color' ? undefined : 'color' });
+        }
+    };
+
+    toggleClip = () => {
+        this.setState({ action: this.state.action === 'clip' ? undefined : 'clip' });
+    };
+
+    highlight = (e: React.MouseEvent<HTMLElement>) => {
+        e.preventDefault();
+        this.plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+        const repr = this.cell?.obj?.data.repr;
+        if (repr) {
+            this.plugin.canvas3d?.mark({ repr, loci: EveryLoci }, MarkerAction.Highlight);
+        }
+        e.currentTarget.blur();
+    };
+
+    clearHighlight = (e: React.MouseEvent<HTMLElement>) => {
+        e.preventDefault();
+        this.plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+        e.currentTarget.blur();
+    };
+
+    toggleSelect = (e: React.MouseEvent<HTMLElement>) => {
+        e.preventDefault();
+        const cell = this.cell as StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D> | undefined;
+        if (!(cell?.obj?.data.sourceData instanceof Structure)) return;
+
+        const loci = Structure.toStructureElementLoci(cell.obj.data.sourceData);
+        this.plugin.managers.interactivity.lociSelects.toggle({ loci }, false);
+    };
+
+    center = (e: React.MouseEvent<HTMLElement>) => {
+        e.preventDefault();
+        const cell = this.cell as StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D> | undefined;
+        if (!(cell?.obj?.data.sourceData instanceof Structure)) return;
+
+        const loci = Structure.toStructureElementLoci(cell.obj.data.sourceData);
+        centerLoci(this.plugin, loci);
+    };
+
+    handleClick = (e: React.MouseEvent<HTMLElement>) => {
+        if (e.ctrlKey) {
+            this.toggleSelect(e);
+        } else {
+            this.center(e);
+        }
+    };
+
+    get colorValue(): Color | undefined {
+        return this.cell.transform.params?.colorTheme?.params.value ?? this.cell.transform.params?.coloring?.params.color;
+    }
+
+    get lightnessValue(): { lightness: number } | undefined {
+        return {
+            lightness: this.cell.transform.params?.colorTheme?.params.lightness ?? this.cell.transform.params?.coloring?.params.lightness ?? 0
+        };
+    }
+
+    get opacityValue(): { alpha: number } | undefined {
+        return {
+            alpha: this.cell.transform.params?.type?.params.alpha ?? this.cell.transform.params?.alpha ?? 1
+        };
+    }
+
+    get emissiveValue(): { emissive: number } | undefined {
+        return {
+            emissive: this.cell.transform.params?.type?.params.emissive ?? this.cell.transform.params?.emissive ?? 0
+        };
+    }
+
+    get clipValue(): Clip.Props | undefined {
+        return this.cell.transform.params.type?.params.clip ?? this.cell.transform.params.clip;
+    }
+
+    get lodValue(): PD.Values<typeof LodParams> | undefined {
+        const p = this.cell.transform.params?.type?.params;
+        if (!p) return;
+        return {
+            lodLevels: p.lodLevels,
+            cellSize: p.cellSize,
+            batchSize: p.batchSize,
+            approximate: p.approximate,
+        };
+    }
+
+    get patternValue(): { amplitude: number, frequency: number } | undefined {
+        const p = this.cell.transform.params;
+        if (p.type) return;
+        return {
+            amplitude: p.bumpAmplitude,
+            frequency: p.bumpFrequency * 10,
+        };
+    }
+
+    updateColor: ParamOnChange = ({ value }) => {
+        const update = this.plugin.state.data.build();
+        for (const g of this.groups) {
+            update.to(g.transform.ref).update(old => {
+                old.color.type = 'custom';
+            });
+        }
+        for (const r of this.roots) {
+            update.to(r).update(old => {
+                old.color.type = 'custom';
+            });
+        }
+        update.to(this.ref).update(old => {
+            if (old.colorTheme) {
+                old.colorTheme.params.value = value;
+            } else if (old.coloring) {
+                old.coloring.params.color = value;
+            }
+        });
+        update.commit();
+    };
+
+    updateLightness = (values: PD.Values) => {
+        return this.plugin.build().to(this.ref).update(old => {
+            if (old.colorTheme) {
+                old.colorTheme.params.lightness = values.lightness;
+            } else if (old.coloring) {
+                old.coloring.params.lightness = values.lightness;
+            }
+        }).commit();
+    };
+
+    updateOpacity = (values: PD.Values) => {
+        return this.plugin.build().to(this.ref).update(old => {
+            if (old.type) {
+                old.type.params.alpha = values.alpha;
+                old.type.params.xrayShaded = values.alpha < 1 ? 'inverted' : false;
+            } else {
+                old.alpha = values.alpha;
+                old.xrayShaded = values.alpha < 1 ? true : false;
+            }
+        }).commit();
+    };
+
+    updateEmissive = (values: PD.Values) => {
+        return this.plugin.build().to(this.ref).update(old => {
+            if (old.type) {
+                old.type.params.emissive = values.emissive;
+            } else {
+                old.emissive = values.emissive;
+            }
+        }).commit();
+    };
+
+    updateClip = (props: Clip.Props) => {
+        const params = this.cell.transform.params;
+        const clip = params.type ? params.type.params.clip : params.clip;
+        if (!PD.areEqual(Clip.Params, clip, props)) {
+            this.plugin.build().to(this.ref).update(old => {
+                if (old.type) {
+                    old.type.params.clip = props;
+                } else {
+                    old.clip = props;
+                }
+            }).commit();
+        }
+    };
+
+    updateLod = (values: PD.Values) => {
+        const params = this.cell.transform.params as StateTransformer.Params<StructureRepresentation3D>;
+        if (!params.type) return;
+
+        MesoscaleState.set(this.plugin, { graphics: 'custom' });
+        (this.plugin.customState as MesoscaleExplorerState).graphicsMode = 'custom';
+
+        if (!deepEqual(params.type.params.lodLevels, values.lodLevels) || params.type.params.cellSize !== values.cellSize || params.type.params.batchSize !== values.batchSize || params.type.params.approximate !== values.approximate) {
+            this.plugin.build().to(this.ref).update(old => {
+                old.type.params.lodLevels = values.lodLevels;
+                old.type.params.cellSize = values.cellSize;
+                old.type.params.batchSize = values.batchSize;
+                old.type.params.approximate = values.approximate;
+            }).commit();
+        }
+    };
+
+    updatePattern = (values: PD.Values) => {
+        return this.plugin.build().to(this.ref).update(old => {
+            if (!old.type) {
+                old.bumpAmplitude = values.amplitude;
+                old.bumpFrequency = values.frequency / 10;
+            }
+        }).commit();
+    };
+
+    render() {
+        const cellState = this.cell.state;
+        const disabled = this.cell.status !== 'error' && this.cell.status !== 'ok';
+        const depth = this.props.depth;
+        const colorValue = this.colorValue;
+        const lightnessValue = this.lightnessValue;
+        const opacityValue = this.opacityValue;
+        const emissiveValue = this.emissiveValue;
+        const lodValue = this.lodValue;
+        const patternValue = this.patternValue;
+
+        const l = getEntityLabel(this.plugin, this.cell);
+        const label = <Button className={`msp-btn-tree-label msp-type-class-${this.cell.obj!.type.typeClass}`} noOverflow disabled={disabled}
+            onClick={this.handleClick}
+            onMouseEnter={this.highlight}
+            onMouseLeave={this.clearHighlight}
+        >
+            <span title={l}>{l}</span>
+        </Button>;
+
+        const color = colorValue !== undefined && <Button style={{ backgroundColor: Color.toStyle(colorValue), minWidth: 32, width: 32, borderRight: `6px solid ${Color.toStyle(Color.lighten(colorValue, lightnessValue?.lightness || 0))}` }} onClick={this.toggleColor} />;
+        const clip = <IconButton svg={ContentCutSvg} toggleState={false} disabled={disabled} small onClick={this.toggleClip} />;
+        const visibility = <IconButton svg={cellState.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg} toggleState={false} disabled={disabled} small onClick={this.toggleVisible} />;
+
+        return <>
+            <div className={`msp-flex-row`} style={{ margin: `1px 5px 1px ${depth * 10 + 5}px` }}>
+                {label}
+                {color}
+                {clip}
+                {visibility}
+            </div>
+            {this.state.action === 'color' && colorValue !== void 0 && <div style={{ marginRight: 5 }} className='msp-accent-offset'>
+                <ControlGroup header='Color' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleColor}
+                    topRightIcon={CloseSvg} noTopMargin childrenClassName='msp-viewport-controls-panel-controls'>
+                    <CombinedColorControl param={ColorValueParam} value={colorValue ?? Color(0xFFFFFF)} onChange={this.updateColor} name='color' hideNameRow />
+                    <ParameterControls params={LightnessParams} values={lightnessValue} onChangeValues={this.updateLightness} />
+                    <ParameterControls params={OpacityParams} values={opacityValue} onChangeValues={this.updateOpacity} />
+                    <ParameterControls params={EmissiveParams} values={emissiveValue} onChangeValues={this.updateEmissive} />
+                    {patternValue && <ParameterControls params={PatternParams} values={patternValue} onChangeValues={this.updatePattern} />}
+                </ControlGroup>
+            </div>}
+            {this.state.action === 'clip' && <div style={{ marginRight: 5 }} className='msp-accent-offset'>
+                <ControlGroup header='Clip' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleClip}
+                    topRightIcon={CloseSvg} noTopMargin childrenClassName='msp-viewport-controls-panel-controls'>
+                    <ParameterMappingControl mapping={this.clipMapping} />
+                    {lodValue && <ParameterControls params={LodParams} values={lodValue} onChangeValues={this.updateLod} />}
+                </ControlGroup>
+            </div>}
+        </>;
+    }
+}
+
+

src/apps/mesoscale-explorer/ui/panels.tsx

@@ -0,0 +1,98 @@
+/**
+ * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mp4EncoderUI } from '../../../extensions/mp4-export/ui';
+import { PluginUIComponent } from '../../../mol-plugin-ui/base';
+import { SectionHeader } from '../../../mol-plugin-ui/controls/common';
+import { MesoscaleExplorerState } from '../app';
+import { MesoscaleState } from '../data/state';
+import { EntityControls, ModelInfo, SelectionInfo } from './entities';
+import { LoaderControls, ExampleControls, SessionControls, SnapshotControls, DatabaseControls } from './states';
+
+const Spacer = () => <div style={{ height: '2em' }} />;
+
+export class LeftPanel extends PluginUIComponent {
+    render() {
+        const customState = this.plugin.customState as MesoscaleExplorerState;
+
+        return <div className='msp-scrollable-container'>
+            <SectionHeader title='Database' />
+            <DatabaseControls />
+            <Spacer />
+
+            <SectionHeader title='Open' />
+            <LoaderControls />
+            <Spacer />
+
+            {customState.examples?.length && <>
+                <SectionHeader title='Example' />
+                <ExampleControls />
+                <Spacer />
+            </>}
+
+            <SectionHeader title='Session' />
+            <SessionControls />
+            <Spacer />
+
+            <SectionHeader title='Snapshots' />
+            <SnapshotControls />
+            <Spacer />
+
+            <Mp4EncoderUI />
+        </div>;
+    }
+}
+
+export class RightPanel extends PluginUIComponent<{}, { isDisabled: boolean }> {
+    state = {
+        isDisabled: false,
+    };
+
+    get hasModelInfo() {
+        return (
+            MesoscaleState.has(this.plugin) &&
+            !!(MesoscaleState.get(this.plugin).description ||
+                MesoscaleState.get(this.plugin).link)
+        );
+    }
+
+    componentDidMount() {
+        this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
+            this.setState({ isDisabled: v });
+        });
+
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (!this.state.isDisabled && MesoscaleState.has(this.plugin) && MesoscaleState.ref(this.plugin) === e.ref) {
+                this.forceUpdate();
+            }
+        });
+
+        this.subscribe(this.plugin.managers.structure.selection.events.changed, e => {
+            if (!this.state.isDisabled) {
+                this.forceUpdate();
+            }
+        });
+    }
+
+    render() {
+        return <div className='msp-scrollable-container'>
+            {this.hasModelInfo && <>
+                <SectionHeader title='Model' />
+                <ModelInfo />
+                <Spacer />
+            </>}
+
+            <>
+                <SectionHeader title='Selection' />
+                <SelectionInfo />
+                <Spacer />
+            </>
+
+            <SectionHeader title='Entities' />
+            <EntityControls />
+        </div>;
+    }
+}

src/apps/mesoscale-explorer/ui/states.tsx

@@ -0,0 +1,363 @@
+/**
+ * Copyright (c) 2022-2023 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 { MmcifProvider } from '../../../mol-plugin-state/formats/trajectory';
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { PluginUIComponent } from '../../../mol-plugin-ui/base';
+import { Button, ExpandGroup } from '../../../mol-plugin-ui/controls/common';
+import { GetAppSvg, Icon, OpenInBrowserSvg } from '../../../mol-plugin-ui/controls/icons';
+import { ApplyActionControl } from '../../../mol-plugin-ui/state/apply-action';
+import { LocalStateSnapshotList, LocalStateSnapshotParams, LocalStateSnapshots } from '../../../mol-plugin-ui/state/snapshots';
+import { PluginCommands } from '../../../mol-plugin/commands';
+import { PluginContext } from '../../../mol-plugin/context';
+import { StateAction, StateObjectRef, StateTransform } from '../../../mol-state';
+import { Task } from '../../../mol-task';
+import { Color } from '../../../mol-util/color/color';
+import { getFileNameInfo } from '../../../mol-util/file-info';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { ExampleEntry, MesoscaleExplorerState } from '../app';
+import { createCellpackHierarchy } from '../data/cellpack/preset';
+import { createGenericHierarchy } from '../data/generic/preset';
+import { createMmcifHierarchy } from '../data/mmcif/preset';
+import { createPetworldHierarchy } from '../data/petworld/preset';
+import { MesoscaleState, MesoscaleStateObject, setGraphicsCanvas3DProps } from '../data/state';
+
+function adjustPluginProps(ctx: PluginContext) {
+    ctx.managers.interactivity.setProps({ granularity: 'chain' });
+    ctx.canvas3d?.setProps({
+        multiSample: { mode: 'off' },
+        cameraClipping: { far: false, minNear: 50 },
+        sceneRadiusFactor: 2,
+        renderer: {
+            colorMarker: true,
+            highlightColor: Color(0xffffff),
+            highlightStrength: 0,
+            selectColor: Color(0xffffff),
+            selectStrength: 0,
+            dimColor: Color(0xffffff),
+            dimStrength: 1,
+            markerPriority: 2,
+            interiorColorFlag: false,
+            interiorDarkening: 0.15,
+            exposure: 1.1,
+            xrayEdgeFalloff: 3,
+        },
+        marking: {
+            enabled: true,
+            highlightEdgeColor: Color(0x999999),
+            selectEdgeColor: Color(0xffff00),
+            highlightEdgeStrength: 1,
+            selectEdgeStrength: 1,
+            ghostEdgeStrength: 1,
+            innerEdgeFactor: 2.5,
+            edgeScale: 2,
+        },
+        postprocessing: {
+            occlusion: {
+                name: 'on',
+                params: {
+                    samples: 32,
+                    multiScale: {
+                        name: 'on',
+                        params: {
+                            levels: [
+                                { radius: 2, bias: 1.0 },
+                                { radius: 5, bias: 1.0 },
+                                { radius: 8, bias: 1.0 },
+                                { radius: 11, bias: 1.0 },
+                            ],
+                            nearThreshold: 10,
+                            farThreshold: 1500,
+                        }
+                    },
+                    radius: 5,
+                    bias: 1,
+                    blurKernelSize: 11,
+                    resolutionScale: 1,
+                    color: Color(0x000000),
+                }
+            },
+            shadow: {
+                name: 'on',
+                params: {
+                    bias: 0.6,
+                    maxDistance: 80,
+                    steps: 3,
+                    tolerance: 1.0,
+                }
+            },
+            outline: {
+                name: 'on',
+                params: {
+                    scale: 1,
+                    threshold: 0.15,
+                    color: Color(0x000000),
+                    includeTransparent: false,
+                }
+            }
+        }
+    });
+
+    const { graphics } = MesoscaleState.get(ctx);
+    setGraphicsCanvas3DProps(ctx, graphics);
+}
+
+async function createHierarchy(ctx: PluginContext, ref: string) {
+    const parsed = await MmcifProvider.parse(ctx, ref);
+
+    const tr = StateObjectRef.resolveAndCheck(ctx.state.data, parsed.trajectory)?.obj?.data;
+    if (!tr) throw new Error('no trajectory');
+
+    if (!MmcifFormat.is(tr.representative.sourceData)) {
+        throw new Error('not mmcif');
+    }
+
+    const { frame, db } = tr.representative.sourceData.data;
+
+    let hasCellpackAssemblyMethodDetails = false;
+    const { method_details } = db.pdbx_struct_assembly;
+    for (let i = 0, il = method_details.rowCount; i < il; ++i) {
+        if (method_details.value(i).toUpperCase() === 'CELLPACK') {
+            hasCellpackAssemblyMethodDetails = true;
+            break;
+        }
+    }
+
+    if (frame.categories.pdbx_model) {
+        await createPetworldHierarchy(ctx, parsed.trajectory);
+    } else if (
+        frame.header.toUpperCase().includes('CELLPACK') ||
+        hasCellpackAssemblyMethodDetails
+    ) {
+        await createCellpackHierarchy(ctx, parsed.trajectory);
+    } else {
+        await createMmcifHierarchy(ctx, parsed.trajectory);
+    }
+}
+
+async function reset(ctx: PluginContext) {
+    const customState = ctx.customState as MesoscaleExplorerState;
+    delete customState.stateRef;
+    customState.stateCache = {};
+    ctx.managers.asset.clear();
+
+    await PluginCommands.State.Snapshots.Clear(ctx);
+    await PluginCommands.State.RemoveObject(ctx, { state: ctx.state.data, ref: StateTransform.RootRef });
+
+    await MesoscaleState.init(ctx);
+    adjustPluginProps(ctx);
+}
+
+export async function loadExampleEntry(ctx: PluginContext, entry: ExampleEntry) {
+    const { url, type } = entry;
+    await loadUrl(ctx, url, type);
+    MesoscaleState.set(ctx, {
+        description: entry.description || entry.label,
+        link: entry.link,
+    });
+}
+
+export async function loadUrl(ctx: PluginContext, url: string, type: 'molx' | 'molj' | 'cif' | 'bcif') {
+    if (type === 'molx' || type === 'molj') {
+        await PluginCommands.State.Snapshots.OpenUrl(ctx, { url, type });
+    } else {
+        await reset(ctx);
+        const isBinary = type === 'bcif';
+        const data = await ctx.builders.data.download({ url, isBinary });
+        await createHierarchy(ctx, data.ref);
+    }
+}
+
+export async function loadPdb(ctx: PluginContext, id: string) {
+    await reset(ctx);
+    const url = `https://models.rcsb.org/${id.toUpperCase()}.bcif`;
+    const data = await ctx.builders.data.download({ url, isBinary: true });
+    await createHierarchy(ctx, data.ref);
+}
+
+export async function loadPdbDev(ctx: PluginContext, id: string) {
+    await reset(ctx);
+    const nId = id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`;
+    const url = `https://pdb-dev.wwpdb.org/bcif/${nId.toUpperCase()}.bcif`;
+    const data = await ctx.builders.data.download({ url, isBinary: true });
+    await createHierarchy(ctx, data.ref);
+}
+
+//
+
+export const LoadDatabase = StateAction.build({
+    display: { name: 'Database', description: 'Load from Database' },
+    params: (a, ctx: PluginContext) => {
+        return {
+            source: PD.Select('pdb', PD.objectToOptions({ pdb: 'PDB', pdbDev: 'PDB-Dev' })),
+            entry: PD.Text(''),
+        };
+    },
+    from: PluginStateObject.Root
+})(({ params }, ctx: PluginContext) => Task.create('Loading from database...', async taskCtx => {
+    if (params.source === 'pdb') {
+        await loadPdb(ctx, params.entry);
+    } else if (params.source === 'pdbDev') {
+        await loadPdbDev(ctx, params.entry);
+    }
+}));
+
+export const LoadExample = StateAction.build({
+    display: { name: 'Load', description: 'Load an example' },
+    params: (a, ctx: PluginContext) => {
+        const entries = (ctx.customState as MesoscaleExplorerState).examples || [];
+        return {
+            entry: PD.Select(0, entries.map((s, i) => [i, s.label])),
+        };
+    },
+    from: PluginStateObject.Root
+})(({ params }, ctx: PluginContext) => Task.create('Loading example...', async taskCtx => {
+    const entries = (ctx.customState as MesoscaleExplorerState).examples || [];
+    await loadExampleEntry(ctx, entries[params.entry]);
+}));
+
+export const LoadModel = StateAction.build({
+    display: { name: 'Load', description: 'Load a model' },
+    params: {
+        files: PD.FileList({ accept: '.cif,.bcif,.cif.gz,.bcif.gz,.zip', multiple: true, description: 'mmCIF or Cellpack- or Petworld-style cif file.', label: 'File(s)' }),
+    },
+    from: PluginStateObject.Root
+})(({ params }, ctx: PluginContext) => Task.create('Loading model...', async taskCtx => {
+    if (params.files === null || params.files.length === 0) {
+        ctx.log.error('No file(s) selected');
+        return;
+    }
+
+    await reset(ctx);
+
+    const firstFile = params.files[0];
+    const firstInfo = getFileNameInfo(firstFile.file!.name);
+
+    if (firstInfo.name.endsWith('zip')) {
+        try {
+            await createGenericHierarchy(ctx, firstFile);
+        } catch (e) {
+            console.error(e);
+            ctx.log.error(`Error opening file '${firstFile.name}'`);
+        }
+    } else {
+        for (const file of params.files) {
+            try {
+                const info = getFileNameInfo(file.file!.name);
+                if (!['cif', 'bcif'].includes(info.ext)) continue;
+
+                const isBinary = ctx.dataFormats.binaryExtensions.has(info.ext);
+                const { data } = await ctx.builders.data.readFile({ file, isBinary });
+                await createHierarchy(ctx, data.ref);
+            } catch (e) {
+                console.error(e);
+                ctx.log.error(`Error opening file '${file.name}'`);
+            }
+        }
+    }
+}));
+
+//
+
+export class DatabaseControls extends PluginUIComponent {
+    componentDidMount() {
+
+    }
+
+    render() {
+        return <div style={{ margin: '5px' }}>
+            <ApplyActionControl state={this.plugin.state.data} action={LoadDatabase} nodeRef={this.plugin.state.data.tree.root.ref} applyLabel={'Load'} hideHeader />
+        </div>;
+    }
+}
+
+export class LoaderControls extends PluginUIComponent {
+    componentDidMount() {
+
+    }
+
+    render() {
+        return <div style={{ margin: '5px' }}>
+            <ApplyActionControl state={this.plugin.state.data} action={LoadModel} nodeRef={this.plugin.state.data.tree.root.ref} applyLabel={'Load'} hideHeader />
+        </div>;
+    }
+}
+
+export class ExampleControls extends PluginUIComponent {
+    componentDidMount() {
+
+    }
+
+    render() {
+        return <div style={{ margin: '5px' }}>
+            <ApplyActionControl state={this.plugin.state.data} action={LoadExample} nodeRef={this.plugin.state.data.tree.root.ref} applyLabel={'Load'} hideHeader />
+        </div>;
+    }
+}
+
+export async function openState(ctx: PluginContext, file: File) {
+    const customState = ctx.customState as MesoscaleExplorerState;
+    delete customState.stateRef;
+    customState.stateCache = {};
+    ctx.managers.asset.clear();
+
+    await PluginCommands.State.Snapshots.Clear(ctx);
+    await PluginCommands.State.Snapshots.OpenFile(ctx, { file });
+
+    const cell = ctx.state.data.selectQ(q => q.ofType(MesoscaleStateObject))[0];
+    if (!cell) throw new Error('Missing MesoscaleState');
+
+    customState.stateRef = cell.transform.ref;
+    customState.graphicsMode = cell.obj?.data.graphics || customState.graphicsMode;
+}
+
+export class SessionControls extends PluginUIComponent {
+    downloadToFileZip = () => {
+        PluginCommands.State.Snapshots.DownloadToFile(this.plugin, { type: 'zip' });
+    };
+
+    open = (e: React.ChangeEvent<HTMLInputElement>) => {
+        if (!e.target.files || !e.target.files[0]) {
+            this.plugin.log.error('No state file selected');
+            return;
+        }
+
+        openState(this.plugin, e.target.files[0]);
+    };
+
+    render() {
+        return <div style={{ margin: '5px' }}>
+            <div className='msp-flex-row'>
+                <Button icon={GetAppSvg} onClick={this.downloadToFileZip} title='Download the state.'>
+                    Download
+                </Button>
+                <div className='msp-btn msp-btn-block msp-btn-action msp-loader-msp-btn-file'>
+                    <Icon svg={OpenInBrowserSvg} inline /> Open <input onChange={this.open} type='file' multiple={false} accept='.molx,.molj' />
+                </div>
+            </div>
+        </div>;
+    }
+}
+
+export class SnapshotControls extends PluginUIComponent<{}> {
+    render() {
+        return <div style={{ margin: '5px' }}>
+            <div style={{ marginBottom: '10px' }}>
+                <LocalStateSnapshotList />
+            </div>
+            <div style={{ marginBottom: '10px' }}>
+                <LocalStateSnapshots />
+            </div>
+
+            <div style={{ marginBottom: '10px' }}>
+                <ExpandGroup header='Snapshot Options' initiallyExpanded={false}>
+                    <LocalStateSnapshotParams />
+                </ExpandGroup>
+            </div>
+        </div>;
+    }
+}

src/apps/viewer/app.ts

@@ -0,0 +1,582 @@
+/**
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
+import { Backgrounds } from '../../extensions/backgrounds';
+import { DnatcoNtCs } from '../../extensions/dnatco';
+import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+import { GeometryExport } from '../../extensions/geo-export';
+import { MAQualityAssessment, QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
+import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
+import { ModelExport } from '../../extensions/model-export';
+import { Mp4Export } from '../../extensions/mp4-export';
+import { MolViewSpec } from '../../extensions/mvs/behavior';
+import { loadMVSX } from '../../extensions/mvs/components/formats';
+import { loadMVS } from '../../extensions/mvs/load';
+import { MVSData } from '../../extensions/mvs/mvs-data';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
+import { RCSBValidationReport } from '../../extensions/rcsb';
+import { AssemblySymmetry, AssemblySymmetryConfig } from '../../extensions/assembly-symmetry';
+import { SbNcbrPartialCharges, SbNcbrPartialChargesPreset, SbNcbrPartialChargesPropertyProvider, SbNcbrTunnels } from '../../extensions/sb-ncbr';
+import { Volseg, VolsegVolumeServerConfig } from '../../extensions/volumes-and-segmentations';
+import { wwPDBChemicalComponentDictionary } from '../../extensions/wwpdb/ccd/behavior';
+import { wwPDBStructConnExtensionFunctions } from '../../extensions/wwpdb/struct-conn';
+import { ZenodoImport } from '../../extensions/zenodo';
+import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
+import { Volume } from '../../mol-model/volume';
+import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
+import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
+import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
+import { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
+import { PluginUIContext } from '../../mol-plugin-ui/context';
+import { createPluginUI } from '../../mol-plugin-ui';
+import { renderReact18 } from '../../mol-plugin-ui/react18';
+import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectRef, StateObjectSelector } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
+import '../../mol-util/polyfill';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { consoleStats, setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
+
+const CustomFormats = [
+    ['g3d', G3dProvider] as const
+];
+
+export const ExtensionMap = {
+    'volseg': PluginSpec.Behavior(Volseg),
+    'backgrounds': PluginSpec.Behavior(Backgrounds),
+    'dnatco-ntcs': PluginSpec.Behavior(DnatcoNtCs),
+    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
+    'assembly-symmetry': PluginSpec.Behavior(AssemblySymmetry),
+    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
+    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
+    'g3d': PluginSpec.Behavior(G3DFormat),
+    'model-export': PluginSpec.Behavior(ModelExport),
+    'mp4-export': PluginSpec.Behavior(Mp4Export),
+    'geo-export': PluginSpec.Behavior(GeometryExport),
+    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
+    'zenodo-import': PluginSpec.Behavior(ZenodoImport),
+    'sb-ncbr-partial-charges': PluginSpec.Behavior(SbNcbrPartialCharges),
+    'wwpdb-chemical-component-dictionary': PluginSpec.Behavior(wwPDBChemicalComponentDictionary),
+    'mvs': PluginSpec.Behavior(MolViewSpec),
+    'tunnels': PluginSpec.Behavior(SbNcbrTunnels),
+};
+
+const DefaultViewerOptions = {
+    customFormats: CustomFormats as [string, DataFormatProvider][],
+    extensions: ObjectKeys(ExtensionMap),
+    disabledExtensions: [] as string[],
+    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: PluginConfig.General.Transparency.defaultValue,
+    preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
+    allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
+    powerPreference: PluginConfig.General.PowerPreference.defaultValue,
+
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
+    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
+    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    viewportShowTrajectoryControls: PluginConfig.Viewport.ShowTrajectoryControls.defaultValue,
+    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,
+    volumesAndSegmentationsDefaultServer: VolsegVolumeServerConfig.DefaultServer.defaultValue,
+    rcsbAssemblySymmetryDefaultServerType: AssemblySymmetryConfig.DefaultServerType.defaultValue,
+    rcsbAssemblySymmetryDefaultServerUrl: AssemblySymmetryConfig.DefaultServerUrl.defaultValue,
+    rcsbAssemblySymmetryApplyColors: AssemblySymmetryConfig.ApplyColors.defaultValue,
+};
+type ViewerOptions = typeof DefaultViewerOptions;
+
+export class Viewer {
+    constructor(public plugin: PluginUIContext) {
+    }
+
+    static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
+        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 ViewerOptions)[]) {
+            if (options[p] !== void 0) definedOptions[p] = options[p];
+        }
+
+        const o: ViewerOptions = { ...DefaultViewerOptions, ...definedOptions };
+        const defaultSpec = DefaultPluginUISpec();
+
+        const disabledExtension = new Set(o.disabledExtensions ?? []);
+
+        const spec: PluginUISpec = {
+            actions: defaultSpec.actions,
+            behaviors: [
+                ...defaultSpec.behaviors,
+                ...o.extensions.filter(e => !disabledExtension.has(e)).map(e => ExtensionMap[e]),
+            ],
+            animations: [...defaultSpec.animations || []],
+            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: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                },
+                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
+            },
+            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.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.DefaultRepresentationPreset, ViewerAutoPreset.id],
+                [PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
+                [VolsegVolumeServerConfig.DefaultServer, o.volumesAndSegmentationsDefaultServer],
+                [AssemblySymmetryConfig.DefaultServerType, o.rcsbAssemblySymmetryDefaultServerType],
+                [AssemblySymmetryConfig.DefaultServerUrl, o.rcsbAssemblySymmetryDefaultServerUrl],
+                [AssemblySymmetryConfig.ApplyColors, o.rcsbAssemblySymmetryApplyColors],
+            ]
+        };
+
+        const element = typeof elementOrId === 'string'
+            ? document.getElementById(elementOrId)
+            : elementOrId;
+        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
+        const plugin = await createPluginUI({
+            target: element,
+            spec,
+            render: renderReact18,
+            onBeforeUIRender: plugin => {
+                // the preset needs to be added before the UI renders otherwise
+                // "Download Structure" wont be able to pick it up
+                plugin.builders.structure.representation.registerPreset(ViewerAutoPreset);
+            }
+        });
+        return new Viewer(plugin);
+    }
+
+    setRemoteSnapshot(id: string) {
+        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
+        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
+    }
+
+    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
+        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
+    }
+
+    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions & { label?: string }) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'url',
+                params: {
+                    url: Asset.Url(url),
+                    format: format as any,
+                    isBinary,
+                    label: options?.label,
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
+                }
+            }
+        }));
+    }
+
+    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+        const plugin = this.plugin;
+
+        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
+    }
+
+    async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
+        const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
+        const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+    }
+
+    loadPdb(pdb: string, options?: LoadStructureOptions) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb' as const,
+                params: {
+                    provider: {
+                        id: pdb,
+                        server: {
+                            name: provider,
+                            params: PdbDownloadProvider[provider].defaultValue as any
+                        }
+                    },
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
+                }
+            }
+        }));
+    }
+
+    loadPdbDev(pdbDev: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'pdb-dev' as const,
+                params: {
+                    provider: {
+                        id: pdbDev,
+                        encoding: 'bcif',
+                    },
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    loadEmdb(emdb: string, options?: { detail?: number }) {
+        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+            source: {
+                name: 'pdb-emd-ds' as const,
+                params: {
+                    provider: {
+                        id: emdb,
+                        server: provider,
+                    },
+                    detail: options?.detail ?? 3,
+                }
+            }
+        }));
+    }
+
+    loadAlphaFoldDb(afdb: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'alphafolddb' as const,
+                params: {
+                    id: afdb,
+                    options: {
+                        ...params.source.params.options,
+                        representation: 'preset-structure-representation-ma-quality-assessment-plddt'
+                    },
+                }
+            }
+        }));
+    }
+
+    loadModelArchive(id: string) {
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+            source: {
+                name: 'modelarchive' as const,
+                params: {
+                    id,
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    }
+
+    /**
+     * @example Load X-ray density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1.5,
+            color: 0x3362B2
+        }, {
+            type: 'relative',
+            value: 3,
+            color: 0x33BB33,
+            volumeIndex: 1
+        }, {
+            type: 'relative',
+            value: -3,
+            color: 0xBB3333,
+            volumeIndex: 1
+        }], {
+            entryId: ['2FO-FC', 'FO-FC'],
+            isLazy: true
+        });
+     * *********************
+     * @example Load EM density from volume server
+        viewer.loadVolumeFromUrl({
+            url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
+            format: 'dscif',
+            isBinary: true
+        }, [{
+            type: 'relative',
+            value: 1,
+            color: 0x3377aa
+        }], {
+            entryId: 'EMD-30210',
+            isLazy: true
+        });
+     */
+    async loadVolumeFromUrl({ url, format, isBinary }: { url: string, format: BuildInVolumeFormat, isBinary: boolean }, isovalues: VolumeIsovalueInfo[], options?: { entryId?: string | string[], isLazy?: boolean }) {
+        const plugin = this.plugin;
+
+        if (!plugin.dataFormats.get(format)) {
+            throw new Error(`Unknown density format: ${format}`);
+        }
+
+        if (options?.isLazy) {
+            const update = this.plugin.build();
+            update.toRoot().apply(StateTransforms.Data.LazyVolume, {
+                url,
+                format,
+                entryId: options?.entryId,
+                isBinary,
+                isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
+            });
+            return update.commit();
+        }
+
+        return plugin.dataTransaction(async () => {
+            const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+
+            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId: options?.entryId });
+            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
+
+            const repr = plugin.build();
+            for (const iso of isovalues) {
+                const volume: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume;
+                const volumeData = volume.cell!.obj!.data;
+                repr
+                    .to(volume)
+                    .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                        type: 'isosurface',
+                        typeParams: { alpha: iso.alpha ?? 1, isoValue: Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
+                        color: 'uniform',
+                        colorParams: { value: iso.color }
+                    }));
+            }
+
+            await repr.commit();
+        });
+    }
+
+    /**
+     * @example
+     *  viewer.loadTrajectory({
+     *      model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
+     *      coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
+     *      preset: 'all-models' // or 'default'
+     *  });
+     */
+    async loadTrajectory(params: LoadTrajectoryParams) {
+        const plugin = this.plugin;
+
+        let model: StateObjectSelector;
+
+        if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
+            const data = params.model.kind === 'model-data'
+                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
+                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
+
+            const trajectory = await plugin.builders.structure.parseTrajectory(data, params.model.format ?? 'mmcif');
+            model = await plugin.builders.structure.createModel(trajectory);
+        } else {
+            const data = params.model.kind === 'topology-data'
+                ? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
+                : await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
+
+            const provider = plugin.dataFormats.get(params.model.format);
+            model = await provider!.parse(plugin, data);
+        }
+
+        const data = params.coordinates.kind === 'coordinates-data'
+            ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
+            : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
+
+        const provider = plugin.dataFormats.get(params.coordinates.format);
+        const coords = await provider!.parse(plugin, data);
+
+        const trajectory = await plugin.build().toRoot()
+            .apply(TrajectoryFromModelAndCoordinates, {
+                modelRef: model.ref,
+                coordinatesRef: coords.ref
+            }, { dependsOn: [model.ref, coords.ref] })
+            .commit();
+
+        const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, params.preset ?? 'default');
+
+        return { model, coords, preset };
+    }
+
+    async loadMvsFromUrl(url: string, format: 'mvsj' | 'mvsx', options?: { replaceExisting?: boolean, keepCamera?: boolean }) {
+        if (format === 'mvsj') {
+            const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'string' }));
+            const mvsData = MVSData.fromMVSJ(data);
+            await loadMVS(this.plugin, mvsData, { sanityChecks: true, sourceUrl: url, ...options });
+        } else if (format === 'mvsx') {
+            const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'binary' }));
+            await this.plugin.runTask(Task.create('Load MVSX file', async ctx => {
+                const parsed = await loadMVSX(this.plugin, ctx, data);
+                await loadMVS(this.plugin, parsed.mvsData, { sanityChecks: true, sourceUrl: parsed.sourceUrl, ...options });
+            }));
+        } else {
+            throw new Error(`Unknown MolViewSpec format: ${format}`);
+        }
+    }
+
+    /** Load MolViewSpec from `data`.
+     * If `format` is 'mvsj', `data` must be a string or a Uint8Array containing a UTF8-encoded string.
+     * If `format` is 'mvsx', `data` must be a Uint8Array or a string containing base64-encoded binary data prefixed with 'base64,'. */
+    async loadMvsData(data: string | Uint8Array, format: 'mvsj' | 'mvsx', options?: { replaceExisting?: boolean, keepCamera?: boolean }) {
+        if (typeof data === 'string' && data.startsWith('base64')) {
+            data = Uint8Array.from(atob(data.substring(7)), c => c.charCodeAt(0)); // Decode base64 string to Uint8Array
+        }
+        if (format === 'mvsj') {
+            if (typeof data !== 'string') {
+                data = new TextDecoder().decode(data); // Decode Uint8Array to string using UTF8
+            }
+            const mvsData = MVSData.fromMVSJ(data);
+            await loadMVS(this.plugin, mvsData, { sanityChecks: true, sourceUrl: undefined, ...options });
+        } else if (format === 'mvsx') {
+            if (typeof data === 'string') {
+                throw new Error("loadMvsData: if `format` is 'mvsx', then `data` must be a Uint8Array or a base64-encoded string prefixed with 'base64,'.");
+            }
+            await this.plugin.runTask(Task.create('Load MVSX file', async ctx => {
+                const parsed = await loadMVSX(this.plugin, ctx, data as Uint8Array);
+                await loadMVS(this.plugin, parsed.mvsData, { sanityChecks: true, sourceUrl: parsed.sourceUrl, ...options });
+            }));
+        } else {
+            throw new Error(`Unknown MolViewSpec format: ${format}`);
+        }
+    }
+
+    handleResize() {
+        this.plugin.layout.events.updated.next(void 0);
+    }
+
+    dispose() {
+        this.plugin.dispose();
+    }
+}
+
+export interface LoadStructureOptions {
+    representationParams?: StructureRepresentationPresetProvider.CommonParams
+}
+
+export interface VolumeIsovalueInfo {
+    type: 'absolute' | 'relative',
+    value: number,
+    color: Color,
+    alpha?: number,
+    volumeIndex?: number
+}
+
+export interface LoadTrajectoryParams {
+    model: { kind: 'model-url', url: string, format?: BuiltInTrajectoryFormat /* mmcif */, isBinary?: boolean }
+    | { kind: 'model-data', data: string | number[] | ArrayBuffer | Uint8Array, format?: BuiltInTrajectoryFormat /* mmcif */ }
+    | { kind: 'topology-url', url: string, format: BuiltInTopologyFormat, isBinary?: boolean }
+    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuiltInTopologyFormat },
+    modelLabel?: string,
+    coordinates: { kind: 'coordinates-url', url: string, format: BuiltInCoordinatesFormat, isBinary?: boolean }
+    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuiltInCoordinatesFormat },
+    coordinatesLabel?: string,
+    preset?: keyof PresetTrajectoryHierarchy
+}
+
+export const ViewerAutoPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-viewer-auto',
+    display: {
+        name: 'Automatic (w/ Annotation)', group: 'Annotation',
+        description: 'Show standard automatic representation but colored by quality assessment (if available in the model).'
+    },
+    isApplicable(a) {
+        return (
+            !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT')) ||
+            !!a.data.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))
+        );
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT'))) {
+            return await QualityAssessmentPLDDTPreset.apply(ref, params, plugin);
+        } else if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))) {
+            return await QualityAssessmentQmeanPreset.apply(ref, params, plugin);
+        } else if (!!structure.models.some(m => SbNcbrPartialChargesPropertyProvider.isApplicable(m))) {
+            return await SbNcbrPartialChargesPreset.apply(ref, params, plugin);
+        } else {
+            return await PresetStructureRepresentations.auto.apply(ref, params, plugin);
+        }
+    }
+});
+
+export const PluginExtensions = {
+    wwPDBStructConn: wwPDBStructConnExtensionFunctions,
+    mvs: { MVSData, loadMVS },
+};

src/apps/viewer/embedded.html

@@ -20,8 +20,8 @@
         <div id="app"></div>
         <script type="text/javascript" src="./molstar.js"></script>
         <script type="text/javascript">
-            var viewer = new molstar.Viewer('app', {
-                layoutIsExpanded: false,
+            molstar.Viewer.create('app', {
+                layoutIsExpanded: true,
                 layoutShowControls: false,
                 layoutShowRemoteState: false,
                 layoutShowSequence: true,
@@ -34,10 +34,20 @@
 
                 pdbProvider: 'rcsb',
                 emdbProvider: 'rcsb',
+            }).then(viewer => {
+                viewer.loadPdb('7bv2');
+                viewer.loadEmdb('EMD-30210', { detail: 6 });
+                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+                // viewer.loadStructureFromUrl('my url', 'pdb', false, {
+                //     representationParams: {
+                //         theme: {
+                //             globalName: 'uniform',
+                //             globalColorParams: { value: 0xff0000 }
+                //         }
+                //     },
+                //     label: 'my structure'
+                // });
             });
-            viewer.loadPdb('7bv2');
-            viewer.loadEmdb('EMD-30210', { detail: 6 });
-            // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
         </script>
     </body>
 </html>

src/apps/viewer/index.html

@@ -46,44 +46,85 @@
             }
 
             var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
-            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
+            if (debugMode) molstar.setDebugMode(debugMode);
+
+            var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
+            if (timingMode) molstar.setTimingMode(timingMode);
 
-            var disableAntialiasing = getParam('disable-antialiasing', '[^&]+').trim() === '1';
-            var pixelScale = parseFloat(getParam('pixel-scale', '[^&]+').trim() || '1');
-            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
-            var viewer = new molstar.Viewer('app', {
-                disableAntialiasing: disableAntialiasing,
-                pixelScale: pixelScale,
-                enableWboit: !disableWboit,
+            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
+            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
+            var pickScale = getParam('pick-scale', '[^&]+').trim();
+            var pickPadding = getParam('pick-padding', '[^&]+').trim();
+            var transparency = getParam('transparency', '[^&]+').trim().toLowerCase();
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+            var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
+            var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
+
+            // console.log('Available extensions: ', Object.keys(molstar.ExtensionMap));
+
+            molstar.Viewer.create('app', {
+                disabledExtensions: [], // anything from Object.keys(molstar.ExtensionMap)
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
+                collapseLeftPanel: collapseLeftPanel,
                 pdbProvider: pdbProvider || 'pdbe',
                 emdbProvider: emdbProvider || 'pdbe',
+                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
+                    ? 'https://maps.rcsb.org'
+                    : 'https://www.ebi.ac.uk/pdbe/densities',
+                pixelScale: parseFloat(pixelScale) || 1,
+                pickScale: parseFloat(pickScale) || 0.25,
+                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
+                transparency: transparency || undefined,
+                preferWebgl1: preferWebgl1,
+                allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
+                powerPreference: powerPreference || 'high-performance',
+            }).then(viewer => {
+                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
+                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
+
+                var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
+                var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
+                if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
+
+                var structureUrl = getParam('structure-url', '[^&]+').trim();
+                var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
+                var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
+                if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
+
+                var mvsUrl = getParam('mvs-url', '[^&]+').trim();
+                var mvsData = getParam('mvs-data', '[^&]+').trim();
+                var mvsFormat = getParam('mvs-format', '[^&]+').trim() || 'mvsj';
+                if (mvsUrl && mvsData) console.error('Cannot specify mvs-url and mvs-data URL parameters at the same time. Ignoring both.');
+                else if (mvsUrl) viewer.loadMvsFromUrl(mvsUrl, mvsFormat);
+                else if (mvsData) viewer.loadMvsData(mvsData, mvsFormat);
+
+
+                var pdb = getParam('pdb', '[^&]+').trim();
+                if (pdb) viewer.loadPdb(pdb);
+
+                var pdbDev = getParam('pdb-dev', '[^&]+').trim();
+                if (pdbDev) viewer.loadPdbDev(pdbDev);
+
+                var emdb = getParam('emdb', '[^&]+').trim();
+                if (emdb) viewer.loadEmdb(emdb);
+
+                var afdb = getParam('afdb', '[^&]+').trim();
+                if (afdb) viewer.loadAlphaFoldDb(afdb);
+
+                var modelArchive = getParam('model-archive', '[^&]+').trim();
+                if (modelArchive) viewer.loadModelArchive(modelArchive);
+
+                window.addEventListener('unload', () => {
+                    // to aid GC
+                    viewer.dispose();
+                });
             });
-
-            var snapshotId = getParam('snapshot-id', '[^&]+').trim();
-            if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
-
-            var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
-            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
-            if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
-
-            var structureUrl = getParam('structure-url', '[^&]+').trim();
-            var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
-            var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
-            if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
-
-            var pdb = getParam('pdb', '[^&]+').trim();
-            if (pdb) viewer.loadPdb(pdb);
-
-            var pdbDev = getParam('pdb-dev', '[^&]+').trim();
-            if (pdbDev) viewer.loadPdbDev(pdbDev);
-
-            var emdb = getParam('emdb', '[^&]+').trim();
-            if (emdb) viewer.loadEmdb(emdb);
         </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
     </body>
 </html>

src/apps/viewer/index.ts

@@ -1,277 +1,12 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import '../../mol-util/polyfill';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import './index.html';
 import './embedded.html';
 import './favicon.ico';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginSpec } from '../../mol-plugin/spec';
-import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
-import { PluginConfig } from '../../mol-plugin/config';
-import { CellPack } from '../../extensions/cellpack';
-import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
-import { PDBeStructureQualityReport } from '../../extensions/pdbe';
-import { Asset } from '../../mol-util/assets';
-import { ObjectKeys } from '../../mol-util/type-helpers';
-import { PluginState } from '../../mol-plugin/state';
-import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
-import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
-import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
-import { DnatcoConfalPyramids } from '../../extensions/dnatco';
-import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
-import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
-import { Color } from '../../mol-util/color';
-import { StateObjectSelector } from '../../mol-state';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
-import { Mp4Export } from '../../extensions/mp4-export';
-import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
-
+import './index.html';
 require('mol-plugin-ui/skin/light.scss');
-
-export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
-export { setProductionMode, setDebugMode } from '../../mol-util/debug';
-
-const CustomFormats = [
-    ['g3d', G3dProvider] as const
-];
-
-const Extensions = {
-    'cellpack': PluginSpec.Behavior(CellPack),
-    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
-    'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
-    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
-    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
-    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
-    'g3d': PluginSpec.Behavior(G3DFormat),
-    'mp4-export': PluginSpec.Behavior(Mp4Export)
-};
-
-const DefaultViewerOptions = {
-    customFormats: CustomFormats as [string, DataFormatProvider][],
-    extensions: ObjectKeys(Extensions),
-    layoutIsExpanded: true,
-    layoutShowControls: true,
-    layoutShowRemoteState: true,
-    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
-    layoutShowSequence: true,
-    layoutShowLog: true,
-    layoutShowLeftPanel: true,
-    disableAntialiasing: false,
-    pixelScale: 1,
-    enableWboit: true,
-
-    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
-    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
-    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
-    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
-    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
-    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,
-};
-type ViewerOptions = typeof DefaultViewerOptions;
-
-export class Viewer {
-    plugin: PluginContext
-
-    constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
-        const o = { ...DefaultViewerOptions, ...options };
-
-        const spec: PluginSpec = {
-            actions: [...DefaultPluginSpec.actions],
-            behaviors: [
-                ...DefaultPluginSpec.behaviors,
-                ...o.extensions.map(e => Extensions[e]),
-            ],
-            animations: [...DefaultPluginSpec.animations || []],
-            customParamEditors: DefaultPluginSpec.customParamEditors,
-            customFormats: o?.customFormats,
-            layout: {
-                initial: {
-                    isExpanded: o.layoutIsExpanded,
-                    showControls: o.layoutShowControls,
-                    controlsDisplay: o.layoutControlsDisplay,
-                },
-                controls: {
-                    ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
-                    top: o.layoutShowSequence ? undefined : 'none',
-                    bottom: o.layoutShowLog ? undefined : 'none',
-                    left: o.layoutShowLeftPanel ? undefined : 'none',
-                }
-            },
-            components: {
-                ...DefaultPluginSpec.components,
-                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
-            },
-            config: [
-                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
-                [PluginConfig.General.PixelScale, o.pixelScale],
-                [PluginConfig.General.EnableWboit, o.enableWboit],
-                [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.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]
-            ]
-        };
-
-        const element = typeof elementOrId === 'string'
-            ? document.getElementById(elementOrId)
-            : elementOrId;
-        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
-        this.plugin = createPlugin(element, spec);
-    }
-
-    setRemoteSnapshot(id: string) {
-        const url = `${this.plugin.config.get(PluginConfig.State.CurrentServer)}/get/${id}`;
-        return PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
-    }
-
-    loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {
-        return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
-    }
-
-    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'url',
-                params: {
-                    url: Asset.Url(url),
-                    format: format as any,
-                    isBinary,
-                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
-                }
-            }
-        }));
-    }
-
-    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
-        const plugin = this.plugin;
-
-        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
-        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
-
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
-    }
-
-    async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
-        const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
-        const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
-    }
-
-    loadPdb(pdb: string, options?: LoadStructureOptions) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'pdb' as const,
-                params: {
-                    provider: {
-                        id: pdb,
-                        server: {
-                            name: provider,
-                            params: PdbDownloadProvider[provider].defaultValue as any
-                        }
-                    },
-                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
-                }
-            }
-        }));
-    }
-
-    loadPdbDev(pdbDev: string) {
-        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
-            source: {
-                name: 'pdb-dev' as const,
-                params: {
-                    provider: {
-                        id: pdbDev,
-                        encoding: 'bcif',
-                    },
-                    options: params.source.params.options,
-                }
-            }
-        }));
-    }
-
-    loadEmdb(emdb: string, options?: { detail?: number }) {
-        const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
-        return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
-            source: {
-                name: 'pdb-emd-ds' as const,
-                params: {
-                    provider: {
-                        id: emdb,
-                        server: provider,
-                    },
-                    detail: options?.detail ?? 3,
-                }
-            }
-        }));
-    }
-
-    async loadVolumeFromUrl(url: string, format: BuildInVolumeFormat, isBinary: boolean, isovalues: VolumeIsovalueInfo[], entryId?: string) {
-        const plugin = this.plugin;
-
-        if (!plugin.dataFormats.get(format)) {
-            throw new Error(`Unknown density format: ${format}`);
-        }
-
-        return plugin.dataTransaction(async () => {
-            const data = await plugin.builders.data.download({ url, isBinary, label: entryId }, { state: { isGhost: true } });
-
-            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId });
-            const volume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
-            if (!volume?.isOk) throw new Error('Failed to parse any volume.');
-
-            const repr = plugin.build().to(volume);
-            for (const iso of isovalues) {
-                repr.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, volume.data!, {
-                    type: 'isosurface',
-                    typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ?  { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
-                    color: 'uniform',
-                    colorParams: { value: iso.color }
-                }));
-            }
-
-            await repr.commit();
-        });
-    }
-
-    handleResize() {
-        this.plugin.layout.events.updated.next();
-    }
-}
-
-export interface LoadStructureOptions {
-    representationParams?: StructureRepresentationPresetProvider.CommonParams
-}
-
-export interface VolumeIsovalueInfo {
-    type: 'absolute' | 'relative',
-    value: number,
-    color: Color,
-    alpha?: number
-}
+export * from './app';

src/cli/chem-comp-dict/create-ions.ts

@@ -1,8 +1,9 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Josh McMenemy <josh.mcmenemy@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import * as argparse from 'argparse';
@@ -14,12 +15,12 @@ const writeFile = util.promisify(fs.writeFile);
 
 import { DatabaseCollection } from '../../mol-data/db';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
-import { ensureDataAvailable, readCCD } from './util';
+import { DefaultDataOptions, ensureDataAvailable, readCCD } from './util';
 
 function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
     const ionNames: string[] = [];
     for (const k in ccd) {
-        const {chem_comp} = ccd[k];
+        const { chem_comp } = ccd[k];
         if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
             ionNames.push(chem_comp.id.value(0));
         }
@@ -31,11 +32,11 @@ function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
 
 function writeIonNamesFile(filePath: string, ionNames: string[]) {
     const output = `/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Code-generated ion names params file. Names extracted from CCD components.
  *
- * @author molstar/chem-comp-dict/create-table cli
+ * @author molstar/chem-comp-dict/create-ions cli
  */
 
 export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
@@ -43,8 +44,8 @@ export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").re
     writeFile(filePath, output);
 }
 
-async function run(out: string, forceDownload = false) {
-    await ensureDataAvailable(forceDownload);
+async function run(out: string, options = DefaultDataOptions) {
+    await ensureDataAvailable(options);
     const ccd = await readCCD();
     const ionNames = extractIonNames(ccd);
     if (!fs.existsSync(path.dirname(out))) {
@@ -54,20 +55,25 @@ async function run(out: string, forceDownload = false) {
 }
 
 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
     description: 'Extract and save IonNames from CCD.'
 });
-parser.addArgument('out', {
+parser.add_argument('out', {
     help: 'Generated file output path.'
 });
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
     help: 'Force download of CCD and PVCD.'
 });
+parser.add_argument('--ccdUrl', '-c', {
+    help: 'Fetch the CCD from a custom URL. This forces download of the CCD.',
+    required: false
+});
 interface Args {
     out: string,
     forceDownload?: boolean,
+    ccdUrl?: string
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
 
-run(args.out, args.forceDownload);
+run(args.out, { forceDownload: args.forceDownload, ccdUrl: args.ccdUrl });

src/cli/chem-comp-dict/create-saccharides.ts

@@ -0,0 +1,82 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse';
+import * as path from 'path';
+import util from 'util';
+import fs from 'fs';
+require('util.promisify').shim();
+const writeFile = util.promisify(fs.writeFile);
+
+import { DatabaseCollection } from '../../mol-data/db';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+import { DefaultDataOptions, ensureDataAvailable, readCCD } from './util';
+
+function extractSaccharideNames(ccd: DatabaseCollection<CCD_Schema>) {
+    const saccharideNames: string[] = [];
+    for (const k in ccd) {
+        const { chem_comp } = ccd[k];
+        const type = chem_comp.type.value(0).toUpperCase();
+        if (type.includes('SACCHARIDE')) {
+            saccharideNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra saccharides that don't have SACCHARIDE in their type
+    saccharideNames.push(
+        'UMQ', // UNDECYL-MALTOSIDE, via GlyFinder
+        'SQD', // SULFOQUINOVOSYLDIACYLGLYCEROL, via GlyFinder
+    );
+    return saccharideNames;
+}
+
+function writeSaccharideNamesFile(filePath: string, ionNames: string[]) {
+    const output = `/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+
+export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+`;
+    writeFile(filePath, output);
+}
+
+async function run(out: string, options = DefaultDataOptions) {
+    await ensureDataAvailable(options);
+    const ccd = await readCCD();
+    const saccharideNames = extractSaccharideNames(ccd);
+    if (!fs.existsSync(path.dirname(out))) {
+        fs.mkdirSync(path.dirname(out));
+    }
+    writeSaccharideNamesFile(out, saccharideNames);
+}
+
+const parser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Extract and save SaccharideNames from CCD.'
+});
+parser.add_argument('out', {
+    help: 'Generated file output path.'
+});
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
+    help: 'Force download of CCD and PVCD.'
+});
+parser.add_argument('--ccdUrl', '-c', {
+    help: 'Fetch the CCD from a custom URL. This forces download of the CCD.',
+    required: false
+});
+interface Args {
+    out: string,
+    forceDownload?: boolean,
+    ccdUrl?: string
+}
+const args: Args = parser.parse_args();
+
+run(args.out, { forceDownload: args.forceDownload, ccdUrl: args.ccdUrl });

src/cli/chem-comp-dict/create-table.ts

@@ -18,7 +18,7 @@ import { SetUtils } from '../../mol-util/set';
 import { DefaultMap } from '../../mol-util/map';
 import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
 import { ccd_chemCompAtom_schema } from '../../mol-io/reader/cif/schema/ccd-extras';
-import { ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
+import { DefaultDataOptions, ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
 
 type CCB = Table<CCD_Schema['chem_comp_bond']>
 type CCA = Table<CCD_Schema['chem_comp_atom']>
@@ -171,7 +171,7 @@ async function createBonds(
         pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant
     });
 
-    const bondDatabase =  Database.ofTables(
+    const bondDatabase = Database.ofTables(
         CCB_TABLE_NAME,
         { chem_comp_bond: mmCIF_chemCompBond_schema },
         { chem_comp_bond: bondTable }
@@ -239,8 +239,8 @@ function createAtoms(ccd: DatabaseCollection<CCD_Schema>, pvcd: DatabaseCollecti
     );
 }
 
-async function run(out: string, binary = false, forceDownload = false, ccaOut?: string) {
-    await ensureDataAvailable(forceDownload);
+async function run(out: string, binary = false, options = DefaultDataOptions, ccaOut?: string) {
+    await ensureDataAvailable(options);
     const ccd = await readCCD();
     const pvcd = await readPVCD();
 
@@ -265,30 +265,40 @@ const CCB_TABLE_NAME = 'CHEM_COMP_BONDS';
 const CCA_TABLE_NAME = 'CHEM_COMP_ATOMS';
 
 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
     description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
 });
-parser.addArgument('out', {
+parser.add_argument('out', {
     help: 'Generated file output path.'
 });
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
     help: 'Force download of CCD and PVCD.'
 });
-parser.addArgument([ '--binary', '-b' ], {
-    action: 'storeTrue',
+parser.add_argument('--binary', '-b', {
+    action: 'store_true',
     help: 'Output as BinaryCIF.'
 });
-parser.addArgument(['--ccaOut', '-a'], {
+parser.add_argument('--ccaOut', '-a', {
     help: 'Optional generated file output path for chem_comp_atom data.',
     required: false
 });
+parser.add_argument('--ccdUrl', '-c', {
+    help: 'Fetch the CCD from a custom URL. This forces download of the CCD.',
+    required: false
+});
+parser.add_argument('--pvcdUrl', '-p', {
+    help: 'Fetch the PVCD from a custom URL. This forces download of the PVCD.',
+    required: false
+});
 interface Args {
     out: string,
     forceDownload?: boolean,
     binary?: boolean,
-    ccaOut?: string
+    ccaOut?: string,
+    ccdUrl?: string,
+    pvcdUrl?: string
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
 
-run(args.out, args.binary, args.forceDownload, args.ccaOut);
+run(args.out, args.binary, { forceDownload: args.forceDownload, ccdUrl: args.ccdUrl, pvcdUrl: args.pvcdUrl }, args.ccaOut);

src/cli/chem-comp-dict/util.ts

@@ -35,9 +35,9 @@ export async function ensureAvailable(path: string, url: string, forceDownload =
     }
 }
 
-export async function ensureDataAvailable(forceDownload = false) {
-    await ensureAvailable(CCD_PATH, CCD_URL, forceDownload);
-    await ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload);
+export async function ensureDataAvailable(options: DataOptions) {
+    await ensureAvailable(CCD_PATH, options.ccdUrl || CCD_URL, !!options.ccdUrl || options.forceDownload);
+    await ensureAvailable(PVCD_PATH, options.pvcdUrl || PVCD_URL, !!options.pvcdUrl || options.forceDownload);
 }
 
 export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
@@ -68,8 +68,18 @@ export function getEncodedCif(name: string, database: Database<Database.Schema>,
     return encoder.getData();
 }
 
+export type DataOptions = {
+    ccdUrl?: string,
+    pvcdUrl?: string,
+    forceDownload?: boolean
+}
+
+export const DefaultDataOptions: DataOptions = {
+    forceDownload: false
+};
+
 const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
 const CCD_PATH = path.join(DATA_DIR, 'components.cif');
 const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
-const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
-const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';
+const CCD_URL = 'https://files.wwpdb.org/pub/pdb/data/monomers/components.cif';
+const PVCD_URL = 'https://files.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';

src/cli/cif2bcif/converter.ts

@@ -70,8 +70,8 @@ function classify(name: string, field: CifField): CifWriter.Field {
     }
 }
 
-export default function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
-    return Task.create<Uint8Array>('BinaryCIF', async ctx => {
+export function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
+    return Task.create<Uint8Array>('Convert CIF', async ctx => {
         const encodingProvider: BinaryEncodingProvider = hints
             ? CifWriter.createEncodingProviderFromJsonConfig(hints)
             : { get: (c, f) => void 0 };

src/cli/cif2bcif/index.ts

@@ -10,7 +10,7 @@ import * as argparse from 'argparse';
 import * as util from 'util';
 import * as fs from 'fs';
 import * as zlib from 'zlib';
-import convert from './converter';
+import { convert } from './converter';
 
 require('util.promisify').shim();
 
@@ -18,7 +18,7 @@ async function process(srcPath: string, outPath: string, configPath?: string, fi
     const config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
     const filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
 
-    const res = await convert(srcPath, false, config, filter);
+    const res = await convert(srcPath, srcPath.toLowerCase().indexOf('.bcif') > 0, config, filter);
     await write(outPath, res);
 }
 
@@ -37,20 +37,20 @@ function run(args: Args) {
 }
 
 const parser = new argparse.ArgumentParser({
-    addHelp: true,
-    description: 'Convert any CIF file to a BCIF file'
+    add_help: true,
+    description: 'Convert any BCIF file to a CIF file or vice versa'
 });
-parser.addArgument([ 'src' ], {
-    help: 'Source CIF path'
+parser.add_argument('src', {
+    help: 'Source file path'
 });
-parser.addArgument([ 'out' ], {
-    help: 'Output BCIF path'
+parser.add_argument('out', {
+    help: 'Output file path'
 });
-parser.addArgument([ '-c', '--config' ], {
+parser.add_argument('-c', '--config', {
     help: 'Optional encoding strategy/precision config path',
     required: false
 });
-parser.addArgument([ '-f', '--filter' ], {
+parser.add_argument('-f', '--filter', {
     help: 'Optional filter whitelist/blacklist path',
     required: false
 });
@@ -61,7 +61,7 @@ interface Args {
     config?: string
     filter?: string
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
 
 if (args) {
     run(args);

src/cli/cifschema/index.ts

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -12,7 +12,7 @@ import fetch from 'node-fetch';
 
 import { parseCsv } from '../../mol-io/reader/csv/parser';
 import { CifFrame, CifBlock } from '../../mol-io/reader/cif';
-import parseText from '../../mol-io/reader/cif/text/parser';
+import { parseCifText } from '../../mol-io/reader/cif/text/parser';
 import { generateSchema } from './util/cif-dic';
 import { generate } from './util/generate';
 import { Filter, Database } from './util/schema';
@@ -28,27 +28,23 @@ function getDicNamespace(block: CifBlock) {
 
 async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
     await ensureMmcifDicAvailable();
-    const mmcifDic = await parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
+    const mmcifDic = await parseCifText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
     if (mmcifDic.isError) throw mmcifDic;
 
     await ensureIhmDicAvailable();
-    const ihmDic = await parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
+    const ihmDic = await parseCifText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
     if (ihmDic.isError) throw ihmDic;
 
-    await ensureCarbBranchDicAvailable();
-    const carbBranchDic = await parseText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
-    if (carbBranchDic.isError) throw carbBranchDic;
-
-    await ensureCarbCompDicAvailable();
-    const carbCompDic = await parseText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
-    if (carbCompDic.isError) throw carbCompDic;
+    await ensureMaDicAvailable();
+    const maDic = await parseCifText(fs.readFileSync(MA_DIC_PATH, 'utf8')).run();
+    if (maDic.isError) throw maDic;
 
     const mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
     const ihmDicVersion = getDicVersion(ihmDic.result.blocks[0]);
-    const carbDicVersion = 'draft';
-    const version = `Dictionary versions: mmCIF ${mmcifDicVersion}, IHM ${ihmDicVersion}, CARB ${carbDicVersion}.`;
+    const maDicVersion = getDicVersion(maDic.result.blocks[0]);
+    const version = `Dictionary versions: mmCIF ${mmcifDicVersion}, IHM ${ihmDicVersion}, MA ${maDicVersion}.`;
 
-    const frames: CifFrame[] = [...mmcifDic.result.blocks[0].saveFrames, ...ihmDic.result.blocks[0].saveFrames, ...carbBranchDic.result.blocks[0].saveFrames, ...carbCompDic.result.blocks[0].saveFrames];
+    const frames: CifFrame[] = [...mmcifDic.result.blocks[0].saveFrames, ...ihmDic.result.blocks[0].saveFrames, ...maDic.result.blocks[0].saveFrames];
     const schema = generateSchema(frames);
 
     await runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases);
@@ -56,7 +52,7 @@ async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, type
 
 async function runGenerateSchemaCifCore(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
     await ensureCifCoreDicAvailable();
-    const cifCoreDic = await parseText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
+    const cifCoreDic = await parseCifText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
     if (cifCoreDic.isError) throw cifCoreDic;
 
     const cifCoreDicVersion = getDicVersion(cifCoreDic.result.blocks[0]);
@@ -80,7 +76,7 @@ async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<
                 if (!file) continue;
                 if (imports.has(file)) continue;
 
-                const dic = await parseText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
+                const dic = await parseCifText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
                 if (dic.isError) throw dic;
 
                 imports.set(file, [...dic.result.blocks[0].saveFrames]);
@@ -92,7 +88,7 @@ async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<
 }
 
 async function runGenerateSchemaDic(name: string, dicPath: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
-    const dic = await parseText(fs.readFileSync(dicPath, 'utf8')).run();
+    const dic = await parseCifText(fs.readFileSync(dicPath, 'utf8')).run();
     if (dic.isError) throw dic;
 
     const dicVersion = getDicVersion(dic.result.blocks[0]);
@@ -124,23 +120,22 @@ async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
     const csvFile = parsed.result;
 
     const fieldNamesCol = csvFile.table.getColumn('0');
-    if (!fieldNamesCol) throw 'error getting fields columns';
+    if (!fieldNamesCol) throw new Error('error getting fields columns');
     const fieldNames = fieldNamesCol.toStringArray();
 
     const filter: Filter = {};
     fieldNames.forEach((name, i) => {
-        const [ category, field ] = name.split('.');
+        const [category, field] = name.split('.');
         // console.log(category, field)
-        if (!filter[ category ]) filter[ category ] = {};
-        filter[ category ][ field ] = true;
+        if (!filter[category]) filter[category] = {};
+        filter[category][field] = true;
     });
     return filter;
 }
 
 async function ensureMmcifDicAvailable() { await ensureDicAvailable(MMCIF_DIC_PATH, MMCIF_DIC_URL); }
 async function ensureIhmDicAvailable() { await ensureDicAvailable(IHM_DIC_PATH, IHM_DIC_URL); }
-async function ensureCarbBranchDicAvailable() { await ensureDicAvailable(CARB_BRANCH_DIC_PATH, CARB_BRANCH_DIC_URL); }
-async function ensureCarbCompDicAvailable() { await ensureDicAvailable(CARB_COMP_DIC_PATH, CARB_COMP_DIC_URL); }
+async function ensureMaDicAvailable() { await ensureDicAvailable(MA_DIC_PATH, MA_DIC_URL); }
 async function ensureCifCoreDicAvailable() {
     await ensureDicAvailable(CIF_CORE_DIC_PATH, CIF_CORE_DIC_URL);
     await ensureDicAvailable(CIF_CORE_ENUM_PATH, CIF_CORE_ENUM_URL);
@@ -163,12 +158,10 @@ async function ensureDicAvailable(dicPath: string, dicUrl: string) {
 const DIC_DIR = path.resolve(__dirname, '../../../../build/dics/');
 const MMCIF_DIC_PATH = `${DIC_DIR}/mmcif_pdbx_v50.dic`;
 const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic';
-const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`;
-const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic';
-const CARB_BRANCH_DIC_PATH = `${DIC_DIR}/entity_branch-extension.dic`;
-const CARB_BRANCH_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/entity_branch-extension.dic';
-const CARB_COMP_DIC_PATH = `${DIC_DIR}/chem_comp-extension.dic`;
-const CARB_COMP_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/chem_comp-extension.dic';
+const IHM_DIC_PATH = `${DIC_DIR}/mmcif_ihm_ext.dic`;
+const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHMCIF/master/dist/mmcif_ihm_ext.dic';
+const MA_DIC_PATH = `${DIC_DIR}/ma-extension.dic`;
+const MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic';
 
 const CIF_CORE_DIC_PATH = `${DIC_DIR}/cif_core.dic`;
 const CIF_CORE_DIC_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic';
@@ -178,44 +171,44 @@ const CIF_CORE_ATTR_PATH = `${DIC_DIR}/templ_attr.cif`;
 const CIF_CORE_ATTR_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif';
 
 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
     description: 'Create schema from mmcif dictionary (v50 plus IHM and entity_branch extensions, downloaded from wwPDB)'
 });
-parser.addArgument([ '--preset', '-p' ], {
-    defaultValue: '',
+parser.add_argument('--preset', '-p', {
+    default: '',
     choices: ['', 'mmCIF', 'CCD', 'BIRD', 'CifCore'],
     help: 'Preset name'
 });
-parser.addArgument([ '--name', '-n' ], {
-    defaultValue: '',
+parser.add_argument('--name', '-n', {
+    default: '',
     help: 'Schema name'
 });
-parser.addArgument([ '--out', '-o' ], {
+parser.add_argument('--out', '-o', {
     help: 'Generated schema output path, if not given printed to stdout'
 });
-parser.addArgument([ '--targetFormat', '-tf' ], {
-    defaultValue: 'typescript-molstar',
+parser.add_argument('--targetFormat', '-tf', {
+    default: 'typescript-molstar',
     choices: ['typescript-molstar', 'json-internal'],
     help: 'Target format'
 });
-parser.addArgument([ '--dicPath', '-d' ], {
-    defaultValue: '',
+parser.add_argument('--dicPath', '-d', {
+    default: '',
     help: 'Path to dictionary'
 });
-parser.addArgument([ '--fieldNamesPath', '-fn' ], {
-    defaultValue: '',
+parser.add_argument('--fieldNamesPath', '-fn', {
+    default: '',
     help: 'Field names to include'
 });
-parser.addArgument([ '--forceDicDownload', '-f' ], {
-    action: 'storeTrue',
+parser.add_argument('--forceDicDownload', '-f', {
+    action: 'store_true',
     help: 'Force download of dictionaries'
 });
-parser.addArgument([ '--moldataImportPath', '-mip' ], {
-    defaultValue: 'molstar/lib/mol-data',
+parser.add_argument('--moldataImportPath', '-mip', {
+    default: 'molstar/lib/mol-data',
     help: 'mol-data import path (for typescript target only)'
 });
-parser.addArgument([ '--addAliases', '-aa' ], {
-    action: 'storeTrue',
+parser.add_argument('--addAliases', '-aa', {
+    action: 'store_true',
     help: 'Add field name/path aliases'
 });
 interface Args {
@@ -230,7 +223,7 @@ interface Args {
     moldataImportPath: string
     addAliases: boolean
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();
 
 const FORCE_DIC_DOWNLOAD = args.forceDicDownload;
 

src/cli/cifschema/util/cif-dic.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -13,15 +13,18 @@ export function getFieldType(type: string, description: string, values?: string[
     switch (type) {
         // mmCIF
         case 'code':
-        case 'ucode':
         case 'line':
-        case 'uline':
         case 'text':
         case 'char':
-        case 'uchar3':
-        case 'uchar1':
         case 'boolean':
             return values && values.length ? EnumCol(values, 'str', description) : StrCol(description);
+        case 'ucode':
+        case 'uline':
+        case 'uchar3':
+        case 'uchar1':
+        case 'uchar5':
+            // only force lower-case for enums
+            return values && values.length ? EnumCol(values.map(x => x.toLowerCase()), 'lstr', description) : StrCol(description);
         case 'aliasname':
         case 'name':
         case 'idname':
@@ -34,8 +37,11 @@ export function getFieldType(type: string, description: string, values?: string[
         case 'seq-one-letter-code':
         case 'author':
         case 'orcid_id':
+        case 'pdbx_PDB_obsoleted_db_id':
+        case 'pdbx_related_db_id':
         case 'sequence_dep':
         case 'pdb_id':
+        case 'pdb_id_u': // should be case insensitve, but can't express that
         case 'emd_id':
         // todo, consider adding specialised fields
         case 'yyyy-mm-dd':
@@ -47,6 +53,7 @@ export function getFieldType(type: string, description: string, values?: string[
         case 'operation_expression':
         case 'point_symmetry':
         case '4x3_matrix':
+        case '3x4_matrix':
         case '3x4_matrices':
         case 'point_group':
         case 'point_group_helical':
@@ -56,6 +63,7 @@ export function getFieldType(type: string, description: string, values?: string[
         case 'symop':
         case 'exp_data_doi':
         case 'asym_id':
+        case 'uniprot_ptm_id':
             return StrCol(description);
         case 'int':
         case 'non_negative_int':
@@ -66,6 +74,7 @@ export function getFieldType(type: string, description: string, values?: string[
         case 'ec-type':
         case 'ucode-alphanum-csv':
         case 'id_list':
+        case 'entity_id_list':
             return ListCol('str', ',', description);
         case 'id_list_spc':
             return ListCol('str', ' ', description);
@@ -79,9 +88,11 @@ export function getFieldType(type: string, description: string, values?: string[
         case 'List(Real,Real)':
         case 'List(Real,Real,Real,Real)':
         case 'Date':
-        case 'Datetime':
+        case 'DateTime':
         case 'Tag':
         case 'Implied':
+        case 'Word':
+        case 'Uri':
             return wrapContainer('str', ',', description, container);
         case 'Real':
             return wrapContainer('float', ',', description, container);
@@ -145,7 +156,7 @@ function getImportFrames(d: Data.CifFrame, imports: Imports) {
 }
 
 /** get field from given or linked category */
-function getField(category: string, field: string, d: Data.CifFrame, imports: Imports, ctx: FrameData): Data.CifField|undefined {
+function getField(category: string, field: string, d: Data.CifFrame, imports: Imports, ctx: FrameData): Data.CifField | undefined {
     const { categories, links } = ctx;
     const cat = d.categories[category];
     if (cat) {
@@ -187,7 +198,7 @@ function getContainer(d: Data.CifFrame, imports: Imports, ctx: FrameData) {
 function getCode(d: Data.CifFrame, imports: Imports, ctx: FrameData): [string, string[] | undefined, string | undefined ] | undefined {
     const code = getField('item_type', 'code', d, imports, ctx) || getField('type', 'contents', d, imports, ctx);
     if (code) {
-        return [ code.str(0), getEnums(d, imports, ctx), getContainer(d, imports, ctx) ];
+        return [code.str(0), getEnums(d, imports, ctx), getContainer(d, imports, ctx)];
     } else {
         console.log(`item_type.code or type.contents not found for '${d.header}'`);
     }
@@ -232,29 +243,26 @@ const FORCE_INT_FIELDS = [
     '_struct_sheet_range.end_auth_seq_id',
 ];
 
+/**
+ * Note that name and mapped name must share a prefix. This is not always the case in
+ * the cifCore dictionary, but for downstream code to work a container field with the
+ * same prefix as the member fields must be given here and in the field names filter
+ * list.
+ */
 const FORCE_MATRIX_FIELDS_MAP: { [k: string]: string } = {
-    'atom_site_aniso.U_11': 'U',
-    'atom_site_aniso.U_22': 'U',
-    'atom_site_aniso.U_33': 'U',
-    'atom_site_aniso.U_23': 'U',
-    'atom_site_aniso.U_13': 'U',
-    'atom_site_aniso.U_12': 'U',
-    'atom_site_aniso.U_11_su': 'U_su',
-    'atom_site_aniso.U_22_su': 'U_su',
-    'atom_site_aniso.U_33_su': 'U_su',
-    'atom_site_aniso.U_23_su': 'U_su',
-    'atom_site_aniso.U_13_su': 'U_su',
-    'atom_site_aniso.U_12_su': 'U_su',
+    'atom_site_aniso.u_11': 'u', // is matrix_u in the the dic
+    'atom_site_aniso.u_22': 'u',
+    'atom_site_aniso.u_33': 'u',
+    'atom_site_aniso.u_23': 'u',
+    'atom_site_aniso.u_13': 'u',
+    'atom_site_aniso.u_12': 'u',
 };
 const FORCE_MATRIX_FIELDS = Object.keys(FORCE_MATRIX_FIELDS_MAP);
 
 const EXTRA_ALIASES: Database['aliases'] = {
-    'atom_site_aniso.U': [
-        'atom_site_anisotrop_U'
-    ],
-    'atom_site_aniso.U_su': [
-        'atom_site_aniso_U_esd',
-        'atom_site_anisotrop_U_esd',
+    'atom_site_aniso.matrix_u': [
+        'atom_site_anisotrop_U',
+        'atom_site_aniso.U'
     ],
 };
 
@@ -317,7 +325,7 @@ export function generateSchema(frames: CifFrame[], imports: Imports = new Map())
     frames.forEach(d => {
         // category definitions in mmCIF start with '_' and don't include a '.'
         // category definitions in cifCore don't include a '.'
-        if (d.header[0] === '_'  || d.header.includes('.')) return;
+        if (d.header[0] === '_' || d.header.includes('.')) return;
         const categoryName = d.header.toLowerCase();
         // console.log(d.header, d.categoryNames, d.categories)
         let descriptionField: Data.CifField | undefined;
@@ -372,7 +380,7 @@ export function generateSchema(frames: CifFrame[], imports: Imports = new Map())
             const parent_name = item_linked.getField('parent_name');
             if (child_name && parent_name) {
                 for (let i = 0; i < item_linked.rowCount; ++i) {
-                    const childName = child_name.str(i);
+                    const childName: string = child_name.str(i);
                     const parentName = parent_name.str(i);
                     if (childName in links && links[childName] !== parentName) {
                         console.log(`${childName} linked to ${links[childName]}, ignoring link to ${parentName}`);

src/cli/cifschema/util/generate.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -8,9 +8,9 @@ import { Database, Filter, Column } from './schema';
 import { indentString } from '../../../mol-util/string';
 import { FieldPath } from '../../../mol-io/reader/cif/schema';
 
-function header (name: string, info: string, moldataImportPath: string) {
+function header(name: string, info: string, moldataImportPath: string) {
     return `/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Code-generated '${name}' schema file. ${info}
  *
@@ -22,7 +22,7 @@ import { Database, Column } from '${moldataImportPath}/db';
 import Schema = Column.Schema;`;
 }
 
-function footer (name: string) {
+function footer(name: string) {
     return `
 export type ${name}_Schema = typeof ${name}_Schema;
 export interface ${name}_Database extends Database<${name}_Schema> {};`;
@@ -35,13 +35,17 @@ function getTypeShorthands(schema: Database, fields?: Filter) {
         const { columns } = schema.tables[table];
         Object.keys(columns).forEach(columnName => {
             if (fields && !fields[table][columnName]) return;
-            types.add(schema.tables[table].columns[columnName].type);
+            const col = schema.tables[table].columns[columnName];
+            if (col.type === 'enum') types.add(col.subType);
+            types.add(col.type);
         });
     });
     const shorthands: string[] = [];
     types.forEach(type => {
         switch (type) {
             case 'str': shorthands.push('const str = Schema.str;'); break;
+            case 'ustr': shorthands.push('const ustr = Schema.ustr;'); break;
+            case 'lstr': shorthands.push('const lstr = Schema.lstr;'); break;
             case 'int': shorthands.push('const int = Schema.int;'); break;
             case 'float': shorthands.push('const float = Schema.float;'); break;
             case 'coord': shorthands.push('const coord = Schema.coord;'); break;
@@ -89,7 +93,7 @@ function doc(description: string, spacesCount: number) {
     ].join('\n');
 }
 
-export function generate (name: string, info: string, schema: Database, fields: Filter | undefined, moldataImportPath: string, addAliases: boolean) {
+export function generate(name: string, info: string, schema: Database, fields: Filter | undefined, moldataImportPath: string, addAliases: boolean) {
     const codeLines: string[] = [];
 
     if (fields) {
@@ -128,7 +132,7 @@ export function generate (name: string, info: string, schema: Database, fields:
         codeLines.push('');
         codeLines.push(`export const ${name}_Aliases = {`);
         Object.keys(schema.aliases).forEach(path => {
-            const [ table, columnName ] = path.split('.');
+            const [table, columnName] = path.split('.');
             if (fields && !fields[table]) return;
             if (fields && !fields[table][columnName]) return;
 

src/cli/cifschema/util/helper.ts

@@ -10,8 +10,8 @@ export function parseImportGet(s: string): Import[] {
     // [{'save':hi_ang_Fox_coeffs  'file':templ_attr.cif}   {'save':hi_ang_Fox_c0  'file':templ_enum.cif}]
     // [{"file":'templ_enum.cif' "save":'H_M_ref'}]
     return s.trim().substring(2, s.length - 2).split(/}[ \n\t]*{/g).map(s => {
-        const save = s.match(/('save'|"save"):([^ \t\n]+)/);
-        const file = s.match(/('file'|"file"):([^ \t\n]+)/);
+        const save = s.match(/('save'|"save"):([^ \t\n{}]+)/);
+        const file = s.match(/('file'|"file"):([^ \t\n{}]+)/);
         return {
             save: save ? save[0].substr(7).replace(/['"]/g, '') : undefined,
             file: file ? file[0].substr(7).replace(/['"]/g, '') : undefined

src/cli/cifschema/util/schema.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -29,8 +29,8 @@ export function FloatCol(description: string): FloatCol { return { type: 'float'
 export type CoordCol = { type: 'coord' } & BaseCol
 export function CoordCol(description: string): CoordCol { return { type: 'coord', description }; }
 
-export type EnumCol = { type: 'enum', subType: 'int' | 'str', values: string[] } & BaseCol
-export function EnumCol(values: string[], subType: 'int' | 'str', description: string): EnumCol {
+export type EnumCol = { type: 'enum', subType: 'int' | 'str' | 'ustr' | 'lstr', values: string[] } & BaseCol
+export function EnumCol(values: string[], subType: 'int' | 'str' | 'ustr' | 'lstr', description: string): EnumCol {
     return { type: 'enum', description, values, subType };
 }
 
@@ -51,13 +51,13 @@ export function ListCol(subType: 'int' | 'str' | 'float' | 'coord', separator: s
 
 export type Filter = { [ table: string ]: { [ column: string ]: true } }
 
-export function mergeFilters (...filters: Filter[]) {
+export function mergeFilters(...filters: Filter[]) {
     const n = filters.length;
     const mergedFilter: Filter = {};
     const fields: Map<string, number> = new Map();
     filters.forEach(filter => {
         Object.keys(filter).forEach(category => {
-            Object.keys(filter[ category ]).forEach(field => {
+            Object.keys(filter[category]).forEach(field => {
                 const key = `${category}.${field}`;
                 const value = fields.get(key) || 0;
                 fields.set(key, value + 1);