molstar

    3.0.1 • Public • Published

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    Mol*

    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 (developed by PDBe) and NGL (developed by RCSB PDB) viewers.

    When using Mol*, please cite:

    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, Nucleic Acids Research, 2021; https://doi.org/10.1093/nar/gkab314.

    Protein Data Bank Integrations

    • The pdbe-molstar library is the Mol* implementation used by EMBL-EBI data resources such as PDBe, PDBe-KB and AlphaFold DB. 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 is the Mol* plugin used by RCSB PDB. The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, rcsb-molstar allows to interactively add or hide of (parts of) chains, as seen in the 3D Protein Feature View.

    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.)
    • mol-math Math related (loosely) algorithms and data structures.
    • 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.
    • mol-model Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).
    • mol-model-formats Data format parsers for mol-model.
    • mol-model-props Common "custom properties".
    • mol-script A scripting language for creating representations/scenes and querying (includes the MolQL query language).
    • mol-geo Creating (molecular) geometries.
    • mol-theme Theming for structure, volume and shape representations.
    • mol-repr Molecular representations for structures, volumes and shapes.
    • 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-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.
    • mol-util Useful things that do not fit elsewhere.

    Moreover, the project contains the implementation of servers, including

    • servers/model A tool for accessing coordinate and annotation data of molecular structures.
    • 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 cli apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).

    Previous Work

    This project builds on experience from previous solutions:

    Building & Running

    Build:

    npm install
    npm run build
    

    Build automatically on file save:

    npm run watch
    

    If working on just the viewer, npm run watch-viewer will provide shorter compile times.

    Build with debug mode enabled:

    DEBUG=molstar npm run watch
    

    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
    

    Run

    If not installed previously:

    npm install -g http-server
    

    ...or a similar solution.

    From the root of the project:

    http-server -p PORT-NUMBER
    

    and navigate to build/viewer

    Code generation

    CIF schemas

    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
    

    Lipid names

    node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
    

    Ion names

    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
    

    GraphQL schemas

    node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
    

    Other scripts

    Create chem comp bond table

    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
    

    Test model server

    export NODE_PATH="lib"; node build/src/servers/model/test.js
    

    State Transformer Docs

    export NODE_PATH="lib"; node build/state-docs
    

    Convert any CIF to BinaryCIF

    node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
    

    To see all available commands, use node lib/commonjs/servers/model/preprocess -h.

    Or

    node lib/commonjs/cli/cif2bcif
    

    Development

    Installation

    If node complains about a missing acorn peer dependency, run the following commands

    npm update acorn --depth 20
    npm dedupe
    

    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.

    "files.associations": {
        "*.glsl.ts": "glsl",
        "*.frag.ts": "glsl",
        "*.vert.ts": "glsl",
        "*.gql.ts": "graphql"
    },
    

    Publish

    Prerelease

    npm version prerelease # assumes the current version ends with '-dev.X'
    npm publish --tag next
    

    Release

    npm version 0.X.0 # provide valid semver string
    npm publish
    

    Deploy

    npm run test
    npm run build
    node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
    

    Contributing

    Just open an issue or make a pull request. All contributions are welcome.

    Funding

    Funding sources include but are not limited to:

    Keywords

    none

    Install

    npm i molstar

    DownloadsWeekly Downloads

    839

    Version

    3.0.1

    License

    MIT

    Unpacked Size

    19.3 MB

    Total Files

    2939

    Last publish

    Collaborators

    • arose
    • dsehnal