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reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["global-illumination","immersive-ar","molecular-graphics","scientific-visualization","virtual-reality","web-graphics","webgl","webgl2","webxr"],"created_at":"2024-11-14T10:16:17.481Z","updated_at":"2026-02-28T23:09:19.003Z","avatar_url":"https://github.com/molstar.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![License](http://img.shields.io/badge/license-MIT-blue.svg?style=flat)](./LICENSE)\n[![npm version](https://badge.fury.io/js/molstar.svg)](https://www.npmjs.com/package/molstar)\n[![Build](https://github.com/molstar/molstar/actions/workflows/node.yml/badge.svg)](https://github.com/molstar/molstar/actions/workflows/node.yml)\n[![Gitter](https://badges.gitter.im/molstar/Lobby.svg)](https://gitter.im/molstar/Lobby)\n\n# Mol*\n\nThe 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.\n\nWhen using Mol*, please cite:\n\nDavid 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.\n\n### Protein Data Bank Integrations\n\n- 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.\n\n- [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).\n\n\n## Project Structure Overview\n\nThe core of Mol* consists of these modules (see under `src/`):\n\n- `mol-task` Computation abstraction with progress tracking and cancellation support.\n- `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)\n- `mol-math` Math related (loosely) algorithms and data structures.\n- `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.\n- `mol-model` Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).\n- `mol-model-formats` Data format parsers for `mol-model`.\n- `mol-model-props` Common \"custom properties\".\n- `mol-script` A scripting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).\n- `mol-geo` Creating (molecular) geometries.\n- `mol-theme` Theming for structure, volume and shape representations.\n- `mol-repr` Molecular representations for structures, volumes and shapes.\n- `mol-gl` A wrapper around WebGL.\n- `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.\n- `mol-state` State representation tree with state saving and automatic updates.\n- `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.\n- `mol-plugin-state` State transformations, builders, and managers.\n- `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.\n- `mol-util` Useful things that do not fit elsewhere.\n\nMoreover, the project contains the implementation of `servers`, including\n\n- `servers/model` A tool for accessing coordinate and annotation data of molecular structures.\n- `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.\n- `servers/plugin-state` A basic server to store Mol* Plugin states.\n\nThe project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).\n\n## Previous Work\nThis project builds on experience from previous solutions:\n- [LiteMol Suite](https://www.litemol.org)\n- [WebChemistry](https://webchem.ncbr.muni.cz)\n- [NGL Viewer](http://nglviewer.org)\n- [MMTF](http://mmtf.rcsb.org)\n- [MolQL](http://molql.org)\n- [PDB Component Library](https://www.ebi.ac.uk/pdbe/pdb-component-library/)\n- And many others (list will be continuously expanded).\n\n## Building \u0026 Running\n\n### Build:\n    npm install\n    npm run build\n\n### Build automatically on file save:\n    npm run watch\n\nIf working on just the viewer, ``npm run watch-viewer`` will provide shorter compile times.\n\n### Build with debug mode enabled:\n    DEBUG=molstar npm run watch\n\nDebug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.\n\n### Cleaning and forcing a full rebuild\n    npm run clean\n\nWipes the `build` and `lib` directories and `.tsbuildinfo` files.\n\n    npm run rebuild\n\nRuns the cleanup script prior to building the project, forcing a full rebuild of the project.\n\nUse these commands to resolve occasional build failures which may arise after some dependency updates. Once done, `npm run build` should work again. Note that full rebuilds take more time to complete.\n\n### Develop with `esbuild`\n\nExperimental support for faster builds with `esbuild`\n- `npm run dev:all` - watch mode for all apps and examples\n- `npm run dev:viewer` - watch mode for viewer\n- `npm run dev:apps` - watch mode for all apps\n- `npm run dev:examples` - watch mode for all examples\n- `npm run dev -- -a \u003capp name 1\u003e \u003capp name 2\u003e -e \u003cexample name 1\u003e ...` - watch mode for specified apps/examples. `-a`/`-e` with without any names will build everything.\n\n### Build for production:\n    NODE_ENV=production npm run build\n\n**Run**\n\nIf not installed previously:\n\n    npm install -g http-server\n\n...or a similar solution.\n\nFrom the root of the project:\n\n    http-server -p PORT-NUMBER\n\nand navigate to `build/viewer`\n\n### Code generation\n**CIF schemas**\n\n    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF\n    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD\n    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD\n    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa\n\n**Lipid names**\n\n    node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts\n\n**Ion names**\n\n    node --max-old-space-size=8192 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts\n\n**Saccharide names**\n\n    node --max-old-space-size=8192 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts\n\n### Other scripts\n**Create chem comp bond table**\n\n    node --max-old-space-size=8192 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b\n\n**Test model server**\n\n    export NODE_PATH=\"lib\"; node build/src/servers/model/test.js\n\n**State Transformer Docs**\n\n    export NODE_PATH=\"lib\"; node build/state-docs\n\n**Convert any CIF to BinaryCIF (or vice versa)**\n\n    node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif\n\nTo see all available commands, use ``node lib/commonjs/servers/model/preprocess -h``.\n\nOr\n\n    node lib/commonjs/cli/cif2bcif\n\nE.g.\n\n    node lib/commonjs/cli/cif2bcif src.cif out.bcif.gz\n    node lib/commonjs/cli/cif2bcif src.bcif.gz out.cif\n\n## Development\n\n### Installation\n\nIf node complains about a missing acorn peer dependency, run the following commands\n\n    npm update acorn --depth 20\n    npm dedupe\n\n### Editor\n\nTo 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.\n\n    \"files.associations\": {\n        \"*.glsl.ts\": \"glsl\",\n        \"*.frag.ts\": \"glsl\",\n        \"*.vert.ts\": \"glsl\"\n    },\n\n## Publish\n\n### Prerelease\n    npm version prerelease # assumes the current version ends with '-dev.X'\n    npm publish --tag next\n\n### Release\n    npm version 0.X.0 # provide valid semver string\n    npm publish\n\n## Deploy\nTo prepare apps and demos for https://molstar.org deploy, run:\n\n    npm run test\n    npm run deploy:local\n\nTo commit these changes remotely to the `molstar/molstar.github.io` repo:\n\n    npm run deploy:remote\n\n## Contributing\nJust open an issue or make a pull request. 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