Newer
Older
[](./LICENSE)
[](https://www.npmjs.com/package/molstar)
[](https://travis-ci.org/molstar/molstar)
[](https://gitter.im/molstar/Lobby)
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).*
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).
David Sehnal
committed
- `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.
David Sehnal
committed
- `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-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.
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).
**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**
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
**GraphQL schemas**
node data/rcsb-graphql/codegen.js
### 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
export NODE_PATH="lib"; node build/src/servers/model/test.js
**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"
npm version prerelease # asumes the current version ends with '-dev.X'
npm publish --tag next
npm version 0.X.0 # provide valid semver string
npm publish
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.