@squonk/data-tier-client v0.1.9

React components for scientific applications

This repository is a collection of re-usable React components that can be used to rapidly create what we term mini-apps, simple applications that are designed with a specific purpose in mind. The initial domain of interest is primarily computational chemistry and cheminformatics.

The repo contains three packages:

• The reusable scientific components
• Services to access the Data-Tier Api
• The InformaticsMatters/Squonk theme

Components

The initial components are in the early design phase and will appear here soon.

We anticipate these categories of component:

• Charting using Plotly
• 3D molecular viewer using NGL Viewer
• Chemical sketcher using JSME (and maybe other sketchers)
• Molecule card view
• Molecular spreadsheet

Some of these components are inspired and partly derived from the Fragalysis and Fragnet Search applications, and most likely will be re-incorporated into those applications as components.

This repo will contain:

1. Source code for each component
2. Documentation and examples for using each component
3. Examples of how to combine components

Data-Tier Api

This is an implementation of the data-tier-api.

A basic implementation of the api endpoints is exposed (ApiService) but this is not meant to be used directly. Extend this class and make use of the methods exposed. A more idiomatic API is exposed in the DataTierApi singleton. This is also a good example of how the ApiService is intended to be implemented.

Theme

This is simply a Mui 4.x theme which is provided to styled-components and exposed as a single Theme provider component. This is optional and is only used on IM/Squonk branded apps.

Example mini-apps

Our first mini-app is nearly ready.

Pose viewer

This allows a SDF file with docking poses and scores to be effectively analysed. The expectation is to be easily able to explore 10's of thousands of poses selecting those to examine in detail using a combination of scores in the SDF file. The selected poses can be compared in 3D in the context of the receptor binding site that is specified as a PDB format file.

There are 4 main re-usable components:

1. A small component that allows to define how to process the input SDF file.
2. A scatter plot component that allows the scores in the SDF file to be visualised and to select molecules of interest.
3. A card view component that shows the molecules selected from the scatter plot as 2D structures along with their properties (scores)
4. A re-usable NGL viewer component that allows to view the 3D poses of the molecules selected from the card view to be viewed in the context of the protein binding site.

Building

This monorepo uses lerna to manage packages. Each package is currently bootstrapped with tsdx.

The following commands are available:

• yarn install to install dependencies
• yarn start to watch for changes and built to the dist directory.
• yarn build to do a one-off build to the dist directory
• yarn test to run any tests that have been created