Skip to content
Snippets Groups Projects
Select Git revision
  • rednatco-v2
  • master default protected
  • rednatco
  • test
  • ntc-tube-uniform-color
  • ntc-tube-missing-atoms
  • restore-vertex-array-per-program
  • watlas2
  • dnatco_new
  • cleanup-old-nodejs
  • webmmb
  • fix_auth_seq_id
  • update_deps
  • ext_dev
  • ntc_balls
  • nci-2
  • plugin
  • bugfix-0.4.5
  • nci
  • servers
  • v0.5.0-dev.1
  • v0.4.5
  • v0.4.4
  • v0.4.3
  • v0.4.2
  • v0.4.1
  • v0.4.0
  • v0.3.12
  • v0.3.11
  • v0.3.10
  • v0.3.9
  • v0.3.8
  • v0.3.7
  • v0.3.6
  • v0.3.5
  • v0.3.4
  • v0.3.3
  • v0.3.2
  • v0.3.1
  • v0.3.0
40 results

molstar

  • Clone with SSH
  • Clone with HTTPS
  • user avatar
    Alexander Rose authored
    e41bb35f
    History

    License Build Status Gitter

    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-theme Molecular representation themeing.
    • mol-repr Molecular representations.
    • 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-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:

    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

    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 limited to: