caddforge-unidock-tools

CADDForge-maintained redistribution of Uni-Dock Tools, with the original unidock_tools import package and unidocktools command. This is an independent redistribution, not an official upstream release. Credit for the implementation remains with the upstream authors.

Release candidate: 1.1.3, based on upstream tag 1.1.3, commit caf3161b28f7ceb5aa3b13bc98a505cb76a39db3, subdirectory unidock_tools. The upstream Python metadata says 0.0.1; this redistribution follows the monorepo release tag for its first maintained release. Future maintained versions evolve independently of upstream. The runtime Python files, templates, and parameter data are unchanged. The bundled AutoGrid executable is rebuilt from the supplied AutoGrid 4.2.9 source with a documented compatibility patch; see its source and build instructions.

python -m pip install caddforge-unidock-tools==1.1.3
unidocktools --help
unidocktools ligandprep --help
unidocktools proteinprep --help

The installation example applies after publication; this candidate is not yet published. The wheel is tagged manylinux_2_28_x86_64 and includes a rebuilt native executable; it is not a portable pure-Python wheel. It requires Linux x86-64 with glibc 2.28 or newer. The GCC OpenMP runtime is linked statically under its Runtime Library Exception; no separate libgomp installation is needed. Building the Python package from its source archive retains that executable and does not add support for other platforms. AutoGrid can also be rebuilt offline from its supplied source. The missing upstream openmm dependency is declared by this redistribution. The Uni-Dock executable / CUDA, AmberTools commands (pdb4amber, reduce, tleap), and optional conformer generators remain separate external software. Before replacing an existing unidock-tools distribution, uninstall it in your environment: the old and renamed distributions share the same import package and CLI and must not be installed together.

The Python implementation retains its Apache-2.0 licence. The bundled AutoGrid executable (version string 4.2.9+caddforge.1) and AD4.1_bound.dat retain GPLv2-or-later terms, reflected in the combined distribution's licence metadata. The statically linked GCC OpenMP runtime retains GPLv3-or-later with the GCC Runtime Library Exception 3.1. See NOTICE and RELEASING.md. Both the wheel and source archive include AutoGrid source, the compatibility patch, provenance, and an offline build script. The wheel installs these under share/caddforge-unidock-tools/autogrid/ in the Python environment. The original binary with unverified corresponding source is excluded from the release artifacts.

Maintained source: idorsia/caddforge-unidock-tools. Report redistribution issues in the maintained issue tracker. Builds and tests run on branches and pull requests; pushing a matching v1.1.3 tag initiates the PyPI release workflow after successful validation.

Upstream documentation

Introduction

Based on Uni-Dock, we have developed several user-friendly and enhanced applications in Uni-Dock Tools. Main features are:

• Individual receptor and ligand preparation applications

• End-to-End Uni-Dock pipeline starting from common formats receptor and ligands

• Multi-Conformation Docking (mcdock): See MCDock Introduction

Installation

Dependency

• Uni-Dock
• Python >= 3.8
• MGLTools, if you want to use AD4 scoring function in Uni-Dock
• MCDock dependencies, see MCDock Installation

Install

Clone Uni-Dock repo, and under unidock_tools subdirectory run pip install .

Or pip install git+https://github.com/dptech-corp/Uni-Dock.git#subdirectory=unidock_tools

Docker

We provide docker image with all the dependencies installed. You can pull the docker image from the following link:

docker pull dptechnology:unidocktools

And run the docker container using the following command:

docker run --gpus 0 -it -v $(pwd):/workpsace unidocktools:v1.0.0 cd /workspace && <Your command>

Applications

1. ProteinPrep

Prepare and Convert PDB-format receptor protein into PDBQT format

unidocktools proteinprep -r <Input PDB File> -o <Output PDBQT File Path>

2. LigandPrep

Prepare ligands to be used in Uni-Dock

unidocktools ligandprep -l <Input SDF ligand files, use commas to seperate> -sd <output_dir> -bs <batch_size=1200>

or write a list of ligand files in a text file and use the following command:

unidocktools ligandprep -i <Txt File> -sd <output_dir>

3. Uni-Dock Pipeline

End-to-End pipeline to run Uni-Dock with common-format receptor and ligands

unidocktools unidock_pipeline -r <receptor file> -l <ligand files> -sd <output_dir> -cx <center_x> -cy <center_y> -cz <center_z>

Parameters

IO Parameters

• -r, --receptor: Path to the receptor file in PDBQT format.
• -l, --ligands: Path to the ligand file in SDF format. For multiple files, separate them by commas.
• -i, --ligand_index: A text file containing the path of ligand files in sdf format.
• -sd, --savedir: Save directory (default: 'unidock_results').

Pocket Parameters

• -cx, --center_x: X-coordinate of the docking box center.
• -cy, --center_y: Y-coordinate of the docking box center.
• -cz, --center_z: Z-coordinate of the docking box center.
• -sx, --size_x: Width of the docking box in the X direction (default: 22.5).
• -sy, --size_y: Width of the docking box in the Y direction (default: 22.5).
• -sz, --size_z: Width of the docking box in the Z direction (default: 22.5).

Docking Parameters

• -sf, --scoring_function: Scoring function (default: 'vina').
• -ex, --exhaustiveness: exhaustiveness (default: 128).
• -ms, --max_step: max_step (default: 20)
• -nm, --num_modes: Number of poses to output (default: 3).
• -rs, --refine_step: Refine step (default: 3).
• -topn, --topn: Top N pose results to keep (default: 100).

Others

• -wd, --workdir: Working directory (default: 'unidock_workdir').
• -bs, --batch_size: Batch size (default: 20).

4. Multi-Conformation Docking (mcdock)

See MCDock Usage

License

The Uni-Dock Tools Python code is Apache-2.0 licensed; see LICENSE. The bundled AutoGrid executable and parameter data have separate GPLv2-or-later terms; see the redistribution notice above.