Web application for haddock3

Haddock3 (High Ambiguity Driven protein-protein DOCKing) is a an information-driven flexible docking approach for the modeling of biomolecular complexes. This software wraps the the haddock3 command line tool in a web application. The web application makes it easy to make a configuration file, run it and show the results.

Uses

• bartender for job execution.
• workflow-builder to construct a Haddock3 workflow config file.
• haddock3 to compute and
  • Its embedded restraints web service is also used.
• haddock3-ui for reusable UI components.

mermaid sequenceDiagram Web app->>+Web app: Login Web app->>+Builder: Construct workflow config Web app->>+Haddock3 restraints web service: Calculate restraints Builder->>+Bartender: Submit job Bartender->>+haddock3 CLI: Run Web app->>+Bartender: State of job Web app->>+Bartender: Result of job

Or in portal mode:

mermaid sequenceDiagram Web app->>+Portal: Login Web app->>+Builder: Construct workflow config Web app->>+Haddock3 restraints web service: Calculate restraints Builder->>+Bartender: Submit job Bartender->>+haddock3 CLI: Run Web app->>+Bartender: State of job Web app->>+Bartender: Result of job

Deployment

Deployments with containers are explained in deploy/README.md. The easiest deployment is with a single worker at deploy/arq/README.mnd.

Setup

The web app is written in Node.js to install dependencies run:

shell npm install

Configuration of the web application is done via .env file or environment variables. For configuration of authentication & authorization see docs/auth.md. For configuration of job submission see docs/bartender.md#configuration. For configuration of how to rewrite the submitted workflow file see docs/rewrite.md. For instructions to run within the BonvinLab computational stuctural biology portal see docs/portal.

Use .env.example as a template:

```shell cp .env.example .env

Edit .env file

```

Create rsa key pair for signing & verifying JWT tokens for bartender web service with:

shell openssl genpkey -algorithm RSA -out private_key.pem \ -pkeyopt rsa_keygen_bits:2048 openssl rsa -pubout -in private_key.pem -out public_key.pem

Bartender web service

The bartender web service should be running if you want to submit jobs. See docs/bartender.md how to set it up.

Haddock3 restraints web service

The scenario forms uses the haddock3 restraints web service. to calculate restraints based on given active residues and structures.

For the web application to use this service, it needs to be running with

```shell

Activated Python environment with haddock3, fastapi and uvicorn installed

uvicorn --port 5000 haddock.clis.restraints.webservice:app ```

If not running on http://localhost:5000 then set the HADDOCK3_RESTRAINTS_URL environment variable.

See docs/scenarios.md for more information on how the web application uses the restraints web service.

Development

For development instructions see CONTRIBUTING.md.

Stack

The tech stack is explained in docs/stack.md.