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 a prototype implementation of this technology (still under development).
Project Overview
The core of Mol* currently consists of these modules:
-
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-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-gl
A wrapper around WebGL. Usesmol-geo
to generate geometries. -
mol-app
Components for builduing UIs. -
mol-view
A reference viewer implementation. -
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
npm run watch-extra
Build/watch mol-viewer
Build
npm run build
npm run build-viewer
Watch
npm run watch
npm run watch-extra
npm run watch-viewer
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
Run via Docker
Build the docker image
docker build -t molstar/proto:httpd .
Run the image
docker run -d -p 80:80 molstar/proto:httpd
Code generation
CIF schemas
node build/node_modules/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/mmcif.ts --fieldNamesPath data/mmcif-field-names.csv --name mmCIF
node build/node_modules/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/ccd.ts --fieldNamesPath data/ccd-field-names.csv --name CCD
node build/node_modules/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/bird.ts --fieldNamesPath data/bird-field-names.csv --name BIRD
node --max-old-space-size=8192 build/node_modules/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
GraphQL schemas
node data/rcsb-graphql/codegen.js
Other scripts
Create chem comp bond table
node --max-old-space-size=8192 build/node_modules/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
Test model server
node build/node_modules/servers/model/test.js
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 limted to:
- RCSB PDB funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE