zendock 0.1.0

a focused Python package for molecular preparation, docking simulation, visualization, and analysis workflows

zendock

zendock is a focused Python package for the molecular docking workflow sketched in Docking.ipynb.

This package aims to provede the entire stack needed to perform molecular docking for scientific use, sacrificing performance and flexibility for access and ease of use.

The base package keeps imports lightweight. Install extras for ligand/receptor preparation, docking, and visualization workflows.

Philosophy

• Lightweight import by default, optional extras for full workflows
• Notebook prototype, package implementation
• uv for development
• pip works for end users

Install

Users

Install from PyPI with regular pip:

pip install zendock

Install the complete workflow stack with:

pip install "zendock[all]"

Targeted extras are also available:

pip install "zendock[prep]"  # ligand/receptor preparation
pip install "zendock[dock]"  # Vina docking
pip install "zendock[viz]"   # 3D/interaction visualization

Development with uv

Create an environment and install the package in editable mode:

uv venv
source .venv/bin/activate
uv pip install -e ".[all]"

Install developer tools too:

uv pip install -e ".[dev]"

Development Workflow

Typical loop:

uv venv
source .venv/bin/activate
uv pip install -e ".[all,dev]"
pytest
python -m build

Project Layout

src/zendock/
  __init__.py
  docking.py
  exceptions.py
  fetching.py
  ligand.py
  models.py
  receptor.py
  result_store.py
  results.py
  tools.py
  utils.py
  workspace.py
tests/
Docking.ipynb
pyproject.toml

Current Public API

from zendock import DockingRunner, Ligand, OutputLayout, Receptor

DockingRunner remains the notebook-friendly facade. New code can pass an OutputLayout to centralize output directories and use the typed result objects cached on runner.last_result after docking.

Visualization Example

from zendock import DockingRunner, Ligand, Receptor

receptor = Receptor(name="egfr", pdb_id="1M17")
# Prepare the receptor, add at least one prepared ligand, and set up Vina first.
runner = DockingRunner(receptor)

runner.run_docking()
runner.export_2d_interaction_diagram("ligand_a")
runner.export_3d_interaction_diagram("ligand_a", pose_index=0)

Notes

• The package is licensed under MIT.