Nanome - Chemical Interactions

A Nanome plugin to Calculate and visualize interatomic contacts between small and macro molecules.

Dependencies

• Docker (https://docs.docker.com/get-docker/)
• (Optional) Docker Compose (https://docs.docker.com/compose/install/)

Deployments

To start the plugin with production settings, we have a script available at ./docker/deploy.sh

./docker/build.sh
./docker/deploy.sh <args>

There's two methods of configuring your plugin.

1) Command Line args.

All Nanome plugins can be configured using the following set of command line args.

user@localhost:~/plugin-chemical-interactions$ python run.py --help
usage: run.py [-h] [-a HOST] [-p PORT] [-r] [-v] [-n NAME [NAME ...]]
              [-k KEYFILE] [-i IGNORE]

Parse Arguments to set up Nanome Plugin

optional arguments:
  -h, --help            show this help message and exit
  -a HOST, --host HOST  connects to NTS at the specified url or IP address
  -p PORT, --port PORT  connects to NTS at the specified port
  -r, --auto-reload     Restart plugin automatically if a .py or .json file in
                        current directory changes
  -v, --verbose         enable verbose mode, to display Logs.debug
  -n NAME [NAME ...], --name NAME [NAME ...]
                        Name to display for this plugin in Nanome
  -k KEYFILE, --keyfile KEYFILE
                        Specifies a key file or key string to use to connect
                        to NTS
  -i IGNORE, --ignore IGNORE
                        To use with auto-reload. All paths matching this
                        pattern will be ignored, use commas to specify
                        several. Supports */?/[seq]/[!seq]

All of these args can be passed to docker/deploy.sh, and will be passed to the plugin container to connect your plugin to the correct NTS.

For example ./docker/deploy.sh -a nts-foobar.example.com -p 5555

When ./docker/deploy.sh is run, the command is copied into docker/redeploy.sh which can be used to redeploy your application without remembering the provided flags.

2) Using a .env file

Alternatively, the chemical-interactions plugin supports storing NTS credentials in a .env file.

First thing you need to do is create a .env file in the top-level directory, which contains NTS connection information

NTS_HOST=foobar.example.com
NTS_PORT=5555

And then running the plugin is as simple as

./docker/deploy.sh --env-file <path to .env file> <plugin_args>

Note that env files can be used alongside plugin args, but -a and -p will always take precedence over NTS_HOST and NTS_PORT

Architecture.

The plugin folder contains the entirety of the application.

• Handles all interactions with Nanome application
• Renders menus
• Visualizes interactions data in VR.

There's a separate conda environment installed in the container, where arpeggio is executed.

• Returns JSON containing interaction results, which is parsed by the plugin.
• See https://github.com/PDBeurope/arpeggio for more.

Development

docker-compose.yml is optimized for development, with debug enabled and the code mounted as volumes.

If you use the VSCode IDE, we provide a .devcontainer, and debug launch configurations to ease development.

License

MIT

References

Harry C Jubb, Alicia P Higueruelo, Bernardo Ochoa-Montaño, Will R Pitt, David B Ascher, Tom L Blundell, Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. Journal of Molecular Biology, Volume 429, Issue 3, 2017, Pages 365-371, ISSN 0022-2836,