Installation

This section provides instructions on how to install OCDocker.

Prerequisites

Make sure you have the following prerequisites installed:

  • Python (>=3.11)

  • Conda (Miniconda/Anaconda) with mamba

  • pip (inside the conda environment)

  • NVIDIA driver/runtime compatible with CUDA 12.8 (required to run Gnina CUDA builds)

Quickstart (minimal, SQLite)

If you want the fastest path without setting up PostgreSQL/MySQL, use SQLite (local file DB) as the backend:

  1. Ensure the system dependencies are installed (see System dependencies).

  2. Create/activate a conda env with Python 3.11 (prefer mamba) and install OCDocker with pip.

  3. Enable SQLite when running commands:

    export OCDOCKER_DB_BACKEND=sqlite
ocdocker doctor

SQLite is recommended for quick experiments and development. PostgreSQL is the default backend, and MySQL is optional for alternative server-based workflows.

System dependencies

Before installing OCDocker, you must install the following system packages on Ubuntu/Debian systems:

sudo apt-get install openbabel libopenbabel-dev swig cmake g++

These packages are required for building and using OpenBabel Python bindings, which are essential for OCDocker’s molecular processing capabilities.

Gnina (CUDA 12.8)

OCDocker expects the Gnina CUDA 12.8 build. To run this binary reliably, ensure:

  • NVIDIA driver is compatible with CUDA 12.8

  • cuDNN 9 runtime is available on the system

Step-by-step installation:

mkdir -p gnina
wget -O gnina/gnina.1.3.2.cuda12.8 \
  https://github.com/gnina/gnina/releases/download/v1.3.2/gnina.1.3.2.cuda12.8
chmod +x gnina/gnina.1.3.2.cuda12.8
sudo install -m 0755 gnina/gnina.1.3.2.cuda12.8 /usr/bin/gnina

Verify:

gnina --version

Note: install.sh already installs this Gnina CUDA 12.8 binary automatically.

Installing OCDocker

To install OCDocker, follow these steps:

  1. Ensure the system dependencies are installed (see System dependencies).

  2. Install mamba (if not already installed):

    conda install -n base -c conda-forge mamba

  3. Create and activate a conda environment:

    mamba create -n ocdocker python=3.11 -y
conda activate ocdocker

  4. Install OCDocker with pip (choose one option):

    Option A: install from PyPI (recommended for users):

    pip install ocdocker

    pip install ocdocker installs the core package only. To install every optional runtime stack, use pip install "ocdocker[all]".

    Optional feature extras:

    # Docking workflows (RDKit/OpenBabel/BioPython)
pip install "ocdocker[docking]"

# Docking + database support (SQLAlchemy + drivers)
pip install "ocdocker[docking,db]"

# ML workflows (PyTorch/XGBoost/Optuna)
pip install "ocdocker[ml]"

# Install all optional runtime features
pip install "ocdocker[all]"

    Option B: install from source (recommended for development):

    git clone https://github.com/Arturossi/OCDocker.git
cd OCDocker
# Base package only
pip install .

# Example: source install with docking + DB extras
pip install -e ".[docking,db]"

Optional: build the Sphinx documentation

If you want to build docs locally in the same ocdocker conda environment:

Option A (conda/mamba):

mamba install -n ocdocker -c conda-forge sphinx sphinx-argparse furo sphinx-rtd-theme myst-parser
make -C docs html

Option B (pip extras):

pip install -e ".[docs]"
make -C docs html