Fragalysis

The "start here" repository for the Fragalysis Stack application. This repository (which is currently UNDER CONSTRUCTION) will be used as a 'base' for all documentation relating to the application.

This replaces the original fragalysis repository, which was responsible for the RDKit-based Python tools for analysis of protein-ligand interactions. The original repository has been renamed and can now be found in the fragalysis-package repository.

The repository is compatible with ReadTheDocs and you can find the latest documentation (built from the most recent changes on this repository's main branch) on ReadTheDocs at https://fragalysis.readthedocs.io/en/latest/.

Stable documentation (built from the most recent tag in this repository) can be found at https://fragalysis.readthedocs.io/en/stable/.

Local development

To compile the documentation, which is based on Sphinx, start with a Python environment (ideally Python 3.12, as that's the version used by ReadTheDocs and the GitHub CI workflow) and install the dependencies: -

python -m venv venv
source venv/bin/activate
pip install --upgrade pip

pip install -r requirements.txt

Then, to build the HTML documentation, run the following command: -

sphinx-build docs/source/ docs/build/

The resulting index.html will be in the docs/build/ directory.

Related repositories

The Fragalysis Stack you find running in Kubernetes relies on a number of related (and diverse) repositories. We've tried to capture references to all of them below, in no particular order: -

xchem respositories

fragalysis-package : Logic that allows connection to the neo4j graph

fragalysis-backend : Django/REST Framework application

fragalysis-frontend : Django visual application (frontend)

fragalysis-stack : The build logic that combines the backed and frontend to create the container image

fragalysis-api : Command-line API utilities

fragalysis-keycloak : A specialised build of keycloak to provide a custom login theme

fragalysis-ispyb-target-access-authenticator : Code for the container image that acts as an interface to ISPyB, yielding Target Access Strings based on username

fragalysis-mock-target-access-authenticator : A "mock" ISPyB authenticator (providing results based on a config file)

fragalysis-rdkit-cartridge-pgvector-debian : An extension to the underlying database image (informaticsmatters/rdkit-cartridge-debian) that adds PG-Vector utilities

fragalysis-stack-kubernetes : Ansible playbooks for application deployment and management

fragalysis-stack-behaviour-tests : Basic gherkin-based behaviour tests for the stack API

xchem-align : Tools to generate input data for Fragalysis

docker-neo4j : Custom neo4j image providing built-in S3 bucket bulk-loading

3rd-party respositories (Informatics Matters)

There are also a number of 3rd-party repositories that provide facilities for the Fragalysis Stack application: -

squonk2-data-manager (PRIVATE) : The Squonk2 Data Manager (a private repository and container image)

squonk2-account-server (PRIVATE) : The Squonk2 Account Server providing accounting and billign services (a private repository and container image)

squonk2-data-manager-ui : The Squonk2 UI

squonk2-data-manager-jupyter-operator : The Squonk2 Jupyter Notebook operator (launches notebooks)

squonk2-data-manager-job-operator : The Squonk2 Job operator (launches Jobs)

squonk2-fragmenstein : Squonk2 Job defintions used by the Fragalysi Stack

Numerous other respositories exist for Job execution etc. For inmformatics Matters any respository that has the topic tag squonk2 or squonk2-jobs might be relevant.

docker-volume-replicator : Replicates volumes (used for media)

bandr : PostgreSQL backup and recovery container images

Fragmentation

There is also the fragmentation logic that is used to compile the underlying neo4j database CSV files. These processes rely on access to substabntial computing resources - typically kubernetes or slurm: -

fragmentor (Informatics Matters) : Standardisation, fragmentation and combination graph logic (and playbooks)

fragmentor-k8s-orchestration (Informatics Matters) : Ansible playbooks for the Kubernetes-based execution of fragmentor Playbooks

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