spock — Standardize, Prepare, Dock

spock is a Python toolkit for structure-based drug design. It bundles a unified molecule/protein storage layer, ligand standardization and preparation pipelines, several docking engines, interaction-fingerprint descriptors, a graph/GNN stack, and an interactive PyMOL GUI — so a target can go from a raw sequence to docked, scored and visualised poses in one place.

Status: active development / beta.

Features

Installation

Requires Python ≥ 3.10. PyMOL (open-source or incentive build) and AutoDock Vina are expected from the environment — the recommended route is conda/micromamba:

# 1. create an environment with the native deps that don't ship cleanly on PyPI
micromamba create -y -n spock -c conda-forge \
    python=3.11 pymol-open-source pyqt pyqtgraph rdkit openbabel plip

# 2. install spock (editable)
git clone https://github.com/CDDLeiden/spock.git
cd spock
micromamba run -n spock pip install -e .

Optional extras:

pip install -e ".[vina]"    # AutoDock Vina Python bindings (CPU docking)
pip install -e ".[gnn]"     # torch, torch_geometric, wandb, ...
pip install -e ".[pymol]"   # GUI helper stack (pypdb, meeko, docker, plip, ...)
pip install -e ".[dev]"     # linting / tests (pre-commit, ruff, pytest)

For Vina-GPU, an NVIDIA Docker runtime is required; see setup_nvidia_docker.sh.

The GUI

Launch the GUI (it runs on PyMOL's own Qt thread) with the installed console script:

spock

or load it as a PyMOL plugin:

pymol spock/gui/addon.py

The interface is organised around a selected target:

All results (structures, ligands, poses, scores) are persisted to the per-target SpockStorage, so closing and reopening a target restores its state.

Tutorials

The tutorial/ folder contains notebooks covering storage creation, standardization, ligand preparation and docking benchmarks.

License & citation

See pyproject.toml for authors and project metadata. Part of the CDD Leiden software stack alongside QSPRpred.