Genesis implementation of Mol*

1. Note that this is a public repo, since we've forked Mol*

2. To make changes and import it to our own environment.

• Create a branch and make changes to it
• Run: npm install and npm run build
• Copy over build/viewer/molstar.js and build/viewer/molstar.css to .../static/scripts/molstar.js and .../static/molstar.css respectively (prefixes hidden for safety)
• Merge branch into the master branch of genesistherapeutics/molstar once genesis DA PR (and this PR?) is approved

ORIGINAL

Mol*

The goal of Mol* (/'mol-star/) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB) viewers.

When using Mol*, please cite:

David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; https://doi.org/10.1093/nar/gkab314.

Protein Data Bank Integrations

• The pdbe-molstar library is the Mol* implementation used by EMBL-EBI data resources such as PDBe, PDBe-KB and AlphaFold DB. This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.

• rcsb-molstar is the Mol* plugin used by RCSB PDB. The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, rcsb-molstar allows to interactively add or hide of (parts of) chains, as seen in the 3D Protein Feature View.

Project Structure Overview

The core of Mol* 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 scripting 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. 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-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 into 3rd party solutions.
• mol-util Useful things that do not fit elsewhere.

Moreover, the project contains the implementation 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 cli 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

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.

Cleaning and forcing a full rebuild

npm run clean

Wipes the build and lib directories and .tsbuildinfo files.

npm run rebuild

Runs the cleanup script prior to building the project, forcing a full rebuild of the project.

Use these commands to resolve occassional build failures which may arise after some dependency updates. Once done, npm run build should work again. Note that full rebuilds take more time to complete.

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

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

Lipid names

node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts

Ion names

node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts

Saccharide names

node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts

GraphQL schemas

node node_modules/@graphql-codegen/cli/cjs/bin -c src/extensions/rcsb/graphql/codegen.yml

Other scripts

Create chem comp bond table

node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/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 (or vice versa)

node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif

To see all available commands, use node lib/commonjs/servers/model/preprocess -h.

Or

node lib/commonjs/cli/cif2bcif

E.g.

node lib/commonjs/cli/cif2bcif src.cif out.bcif.gz
node lib/commonjs/cli/cif2bcif src.bcif.gz out.cif

Development

Installation

If node complains about a missing 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 extensions are installed in the editor.

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

Publish

Prerelease

npm version prerelease # assumes 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.

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
• EntosAI