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 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.
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 formol-model
. -
mol-model-props
Common "custom properties". -
mol-script
A scriting 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. Usesmol-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 utilizingmol-state
andmol-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
- WebChemistry
- NGL Viewer
- MMTF
- MolQL
- 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
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
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
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 funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
- PDBe, EMBL-EBI
- CEITEC