xchem-hippo 1.0.1

Hit Interaction Profiling and Procurement Optimisation

XChem HIPPO

HIPPO: 🦛 Hit Interaction Profiling for Progression Optimisation

HIPPO is in active development and feedback is appreciated.

Please see the documentation to get started

Installation

HIPPO is pip-installable, but use of a conda environment is recommended for the rdkit and chemicalite dependencies:

pip install --upgrade hippo-db
conda install -c conda-forge chemicalite=2024.05.1

For more information see the installation guide

You can verify the installation:

python -m hippo verify

Or by running the full suite of tests (see Developer information)

More Information

Repository structure

Branches

• HIPPO/main: latest stable version
• HIPPO/dev: Dvelopment branch
• HIPPO/postgres: PostgreSQL development branch
• HIPPO/django_lean: An experimental branch implementing HIPPO as a Django web-app

Information for HIPPO developers

Developer installation

To develop on HIPPO please fork this repository and then install locally:

git clone https://github.com/YOUR_USER/HIPPO
cd HIPPO
pip install -e .

Releases

HIPPO is automatically released to PyPI as xchem-hippo via a Github Action off the using the release workflow.

When you want to make an official release go to the Releases page and then click the Draft a new release button. Remember to familiarise yourself with the xchem release process on the trunk-based-development Wiki Creating releases page.

Code style

HIPPO is linted using black and commits are automatically linted using the lint workflow. The use of pre-commit is encouraged for local development to automatically run the linting at git commit time:

pip install pre-commit
pre-commit install

Documentation

Documentation is automatically built off the HIPPO/main branch using readthedocs. For local building using sphinx:

cd docs
make html

To check API reference coverage use docstr-coverage

pip install docstr-coverage
docstr-coverage hippo

Tests

Some tests are provided in the tests directory, which can be run with pytest:

cd tests
pytest

N.B. the numbered tests, e.g. test_00_cleanup.py need to run in sequential order to set up the database. Other tests can run in arbitrary order thereafter. The tests will fail if https://fragalysis.diamond.ac.uk can not provide the protein target's data, as specified in tests/config.py.

Postgres specific instructions

Local Postgres development (Mac)

Install via homebrew

brew install postgresql@18

Initialise database

/opt/homebrew/opt/postgresql@18/bin/initdb -D /opt/homebrew/var/postgresql@18 -U postgres -W

Run in foreground

/opt/homebrew/opt/postgresql@18/bin/postgres -D /opt/homebrew/var/postgresql@18 -p 5432

Install psycopg

pip install psycopg[binary]

See images/postgres for a container including the RDKit cartridge

Connecting to a remote deployment

Check port availability:

nc -zv IP_ADDRESS 5432

Success will look something like this:

Ncat: Version 7.92 ( https://nmap.org/ncat )
Ncat: Connected to IP_ADDRESS:5432.
Ncat: 0 bytes sent, 0 bytes received in 0.01 seconds.

To ssh tunnel to a host which has the correct exposed port and forward the correct port:

ssh -L 5432:IP_ADDRESS:5432 USER@GATEWAY_HOST

To test your connection (from your local machine)

pg_isready -h localhost -p 5432

To list available databases with psql

psql -h localhost -U USER -p 5432 -l

To connect to a specific database with psql

psql -h localhost -U USER -p 5432 -n DATABASE

Running tests

To run the unit tests, uncomment and configure tests/config.py to the desired postgres deployment. N.B. currently not all tests will succeed.