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# Mol*

The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will serve as 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 visualisation tools for macromolecular structure data available from [PDB](https://www.wwpdb.org/) and other institutions.

This particular project is the implementation of this technology (still under development).

*If you are looking for the "MOLeculAR structure annoTator", that package is now available on NPM as [MolArt](https://www.npmjs.com/package/molart).*

## Project Overview

The core of Mol* currently 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 scriting 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-app` Components for builduing 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 to 3rd party solutions.
- `mol-util` Useful things that do not fit elsewhere.

Moreover, the project contains the imlementation 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 basic proof of concept `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.

### 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**
Install CIFTools `npm install ciftools -g`

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

**GraphQL schemas**

    ./node_modules/.bin/graphql-codegen -c ./data/rcsb-graphql/codegen.yml

### Other scripts
**Create chem comp bond table**

    export NODE_PATH="lib"; node --max-old-space-size=4096 lib/apps/chem-comp-bond/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 build/model-server/preprocess -i file.cif -ob file.bcif

To see all available commands, use ``node build/model-server/preprocess -h``.

## Development

### Intallation

If node complains about a missine 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 extanesions are installed in the editor.

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

## Publish

### Prerelease
    npm version prerelease # asumes 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.

## 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/)