In-house version of Salentin's code (https://github.com/ssalentin/plip)

Analyses interactions in 3 steps:

1. Detects atoms and groups with specific properties in the receptor and in the ligand

2. Detects interactions between receptor and ligand

3. Refines interactions to avoid double counts

• Hydrophobic interactions:
  • Remove hydrophobic contacts for atoms that also interact via pi-hydrophobic,
  • Filter out contacts that involve an atom also involved in another hydrophobic interaction
• Pi-Cation interactions:
  • If pi-cation and pi-stacking reported for the same L-P residues, keep the pi-stacking (e.g. histidine rings also positively charged)
• Pi-Hydrophobic interactions:
  • Filter out contacts that involve an atom also involved in another pi-hydrophobic interaction
• H-Bonds:
  • Remove contact if donor AND acceptor form a salt bridge
  • Remove contact if H-bond actually part of a water bridge
  • Remove contact if ligand atom part of a metal complex and H-bond with a binder of that same complex
  • Allow only one H-bond per donor
• Water Bridges:
  • If water bridge with a water involved in a metal complex, keep the metal complex (water molecules coordinated to metals tend to form lots of water bridges and H-bonds just because they are close, but angles can be unrealistic)

After installing poetry, you can install the environment:

poetry install

Don't forget to update the lock file if the dependencies have change:

poetry lock

Pre-commit add a hook before your commit and run flake8, black, mypy and other checks.

To install pre-commit:

brew install pre-commit

To set the hook on the repository

pre-commit install

Useful commands:

# Run tests
poetry run task test

# Indent your files with black
poetry run task black

# Check your code with mypy
poetry run task mypy

# Check style
poetry run task linter