npm package: @inftech/molstar
Description: A comprehensive macromolecular library.
Author: Mol* Contributors
Latest version: 3.17.0-inf.1.1.11

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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](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (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](https://doi.org/10.1093/nar/gkab314), *Nucleic Acids Research*, 2021; https://doi.org/10.1093/nar/gkab314.

### Protein Data Bank Integrations

- 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.)
- `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](https://molql.github.io)).
- `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:
- [LiteMol Suite](https://www.litemol.org)
- [WebChemistry](https://webchem.ncbr.muni.cz)
- [NGL Viewer](http://nglviewer.org)
- [MMTF](http://mmtf.rcsb.org)
- [MolQL](http://molql.org)
- [PDB Component Library](https://www.ebi.ac.uk/pdbe/pdb-component-library/)
- And many others (list will be continuously expanded).

## 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

**Saccharide names**

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

**GraphQL schemas**

    node node_modules/@graphql-codegen/cli/cjs/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 (or vice versa)**

    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

E.g.

    node lib/commonjs/cli/cif2bcif src.cif out.bcif.gz
    node lib/commonjs/cli/cif2bcif src.bcif.gz out.cif

## 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:
* [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)