Nanome - Data Table

A Nanome plugin to view multi-frame structure metadata in a table

Dependencies

Docker

Usage

To run Data Table in a Docker container:

$ cd docker
$ ./build.sh
$ ./deploy.sh [run_args]

Optional arguments

• --https

  Enable HTTPS using a self-signed certificate. If port is not set, port will default to 443.

• -u url or --url url

  The url opened when the plugin is run to access the Web UI. Example: -u table.example.com

• -w port or --web-port port

  The port to use for the Web UI. Example: -w 8080

  Some OSes prevent the default port 80 from being used without elevated permissions, so this option may be used to change to an allowed port.

External Properties

This plugin supports configuration to fetch chemical properties from external sources. To get started, rename the config.example.json to config.json. In that file:

overwrite - true will replace the default properties with the external ones. false will append external properties to the end of the list.
endpoints - list of url endpoints to fetch properties from.

endpoints

An endpoint is a url that can be queried for chemical properties. Each endpoint can be used to populate multiple properties. The currently supported modes are GET smiles, POST smiles, and POST sdf, with a response type of json.

In GET smiles mode, the endpoint url is expected to contain the string :smiles. When this endpoint is queried, the smiles for the chemical in question will replace :smiles. Example: example.com/chem/:smiles or example.com/chem?q=:smiles.

In POST smiles mode, either the payload or query is expected to contain the string :smiles. When this endpoint is queried, the smiles for the chemical in question will replace :smiles. Example: {"smiles":":smiles"}.

name - unique name for the endpoint
url - endpoint url
method - either GET or POST
data - either sdf or smiles
cache_time - time in seconds to cache external properties for same SMILES (default 30)
verify - set to false to disable SSL verification
headers - optional headers object to send with the request
query - optional key-value query params to add to the URL. JSON objects will be serialized and URL-encoded
payload - for POST smiles requests, the payload to send containing :smiles
properties - a mapping of property names to config

properties

The properties configuration allows one endpoint to populate multiple properties. Each property has a path to find the property in the response body. For example, if the endpoint response body is {"properties":{"prop1":1}}, the path would be properties.prop1.

format - format string to format the unit. example "%.3f"
path - path to the property in the response body

path syntax

path supports dot notation, array indexing, and array searching.

path.to.prop - dot notation
path[0] - array indexing
path[key=value] - array searching

Dot notation: if the endpoint response body is {"properties":{"prop1":1}}, the path would be properties.prop1.

Array indexing: if the endpoint response body is {"properties":[1,2]}, the path would be properties[0].

Array searching: if the endpoint response body is {"properties":[{"key":"prop1","value":1},{"key":"prop2","value":2}]}, the path would be properties[key=prop1].value.

Development

To run Data Table with autoreload:

$ python3 -m pip install -r requirements.txt
$ python3 run.py -r [run_args]

License

MIT