The Mini-Apps 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

The application is distributed as a container image, normally built automatically using GitLab Actions. To understand how to build the app refer to the project's various .gitlab/workflows.

Deployment

Container images are automatically deployed from a GitLab Action using Job Templates on our AWX server. The Job Templates are launched using scripts that the Action downloads from our Trigger AWX project.

Application versioning

The application version (defined in package.json) is automatically set from within the Dockerfile. If the tag build argument is not defined the version of the application is 0.0.0.

The CI/CD process in Travis sets the tag to the prevailing git tag. So, to build and push version 1.0.0 tag the repository with 1.0.0.

As a consequence you MUST NOT adjust the version line in the

package.json file.

Development Alongside the component library

Currently the best way to develop apps alongside the component library, squonk-theme and data-tier-client is to

1. Clone the react-sci-components repo,
2. Clone the app into the /packages directory,
3. Run lerna link in the root of react-sci-components
4. In terminal(s) run yarn start inside of the package(s) that are going to be developed

Optionally, ensure the app packages in your VSCode workspace are listed first as VSCode current doesn't handle subrepos that well. For example:

"folders": [
    {
        "path": "packages/pose-viewer"
    },
    {
        "path": "packages/fragnet-ui"
    },
    {
        "path": "."
    },
],

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