Installation#

Requirements#

  • Python >= 3.11

  • Linux or macOS

  • AutoDock-GPU v1.6 (Required for standard benchmark scoring; NVIDIA GPU recommended)

Step 1: Install AutoDock-GPU (Required, v1.6)#

mockdock uses AutoDock-GPU (tested with v1.6) as its primary docking and scoring backend.

Download a pre-compiled binary directly from GitHub Releases or compile from source following the instructions in the AutoDock-GPU repository.

Custom AutoDock-GPU Executable Path#

By default, mockdock searches for an adgpu executable on your system PATH. You can specify a custom binary location using either:

  1. The ADGPU_EXECUTABLE environment variable:

export ADGPU_EXECUTABLE=/custom/path/to/adgpu

  1. Or the adgpu_executable parameter in Python:

from mockdock import MDOracle

oracle = MDOracle("CHK1", adgpu_executable="/custom/path/to/adgpu")

Step 2: Install mockdock#

Install mockdock in editable mode:

git clone https://github.com/Popov-Lab-UNC/mockdock.git
cd mockdock
pip install -e .

Or using uv:

git clone https://github.com/Popov-Lab-UNC/mockdock.git
cd mockdock
uv venv
uv sync

Optional Backends & Extras#

All Optional Dependencies Combined#

To install all optional backends and development/docs tools together:

pip install -e ".[all]"

Or with uv:

uv sync --all-extras

AutoDock Vina Backend (CPU Fallback)#

To enable CPU-based docking via AutoDock Vina (no GPU required):

pip install -e ".[vina]"

Receptor Preparation & Custom Benchmark Tools#

For using standard benchmark targets, pre-computed AutoGrid maps are included and no extra tools are needed.

If you are creating new custom benchmark systems from raw PDB or CIF files:

# Install ProDy for receptor splitting and cleaning
pip install -e ".[receptor]"

# (Optional) Install CCTBX for complex bond-order assignment
conda install -c conda-forge cctbx-base

Building Documentation Locally#

To build these Shibuya Sphinx docs locally:

pip install -r docs/requirements.txt
cd docs
make html

Open docs/_build/html/index.html in your browser.

Cache & Scratch Directory#

mockdock caches global resources (such as downloaded ChEMBL bioactivity datasets and pre-computed AutoGrid files) in a persistent directory.

By default, this is ~/.mockdock/. You can override this path by setting the MOCKDOCK_CACHE_DIR environment variable:

export MOCKDOCK_CACHE_DIR=/path/to/shared/mockdock_cache