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0.334.0

PyPI

acedrg

Stereochemical description generator for ligands

Published2 Sept 2026

Direct dependencies9

Transitive dependenciesNot calculated

README

Version 0.334.0 documentation

AceDRG

AceDRG generates stereochemical descriptions (restraint dictionaries) for ligands and links, for use in macromolecular refinement.

Installation

pip install acedrg

Prebuilt wheels are available for Linux (x86_64), macOS (Apple silicon) and Windows (x64); each wheel bundles the C++ engine (libmol) and the AceDRG stereochemistry tables, so no separate CCP4 installation is required at run time.

Optional extras:

pip install "acedrg[tautomer]"  # tautomer handling via molvs

Usage

acedrg -i "CCO" -o ethanol          # from a SMILES string (or a file of one)
acedrg -m ligand.mol -o my_ligand   # from an MDL mol file
acedrg -s ligand.sdf -o my_ligand   # from an SDF file
acedrg -c ligand.cif -o my_ligand   # from an mmCIF file
acedrg -L link_instructions.txt -o my_link   # covalent link description
acedrg --help                       # full option list

The bundled engine and tables are located automatically under the environment prefix (<prefix>/libexec/libmol, <prefix>/share/acedrg/tables). If a CCP4 environment is active it is used as a fallback.

Building from source

On platforms without a wheel, pip builds from the sdist; you can also install from a clone:

git clone https://github.com/MonomerLibrary/AceDRG
cd AceDRG
pip install .

Requirements:

A C++17 compiler and CMake (>= 3.15)
Python >= 3.8
An internet connection — the stereochemistry tables are fetched during the build from the aceDRG-tables repository

Python dependencies (rdkit, gemmi, networkx, numpy, future, pdbecif, servalcat) are installed automatically.

Tests

pip install ".[tautomer]" pytest
pytest -v python-tests --run-extra

Citation

Long F, Nicholls RA, Emsley P, Gražulis S, Merkys A, Vaitkus A, Murshudov GN (2017). AceDRG: a stereochemical description generator for ligands. Acta Cryst. D 73, 112–122. doi: 10.1107/S2059798317000067

Contributions

AceDRG

Fei Long, Robert A. Nicholls, Paul Emsley, Saulius Gražulis, Andrius Merkys, Antanas Vaitkus, Garib N. Murshudov

Pip installation of AceDRG

Jordan Dialpuri, Lucrezia Catapano, Paul Emsley

Contact

AceDRG: Fei Long — flong@mrclmb.ac.uk
Pip packaging and installation: Jordan Dialpuri — jdialpuri@mrclmb.ac.uk

Bug reports and feature requests are best raised as GitHub issues.

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Declared dependencies 9

Native requirements

9 direct targetsNot calculated transitive count

Package / target	Requirement	Relationship
rdkit Environment { "extras": "", "marker": null, "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`rdkit`	runtime
gemmi Environment { "extras": "", "marker": null, "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`gemmi`	runtime
networkx Environment { "extras": "", "marker": null, "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`networkx`	runtime
numpy Environment { "extras": "", "marker": null, "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`numpy`	runtime
future Environment { "extras": "", "marker": null, "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`future`	runtime
pdbecif Environment { "extras": "", "marker": null, "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`pdbecif`	runtime
servalcat Environment { "extras": "", "marker": null, "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`servalcat`	runtime
metalCoord Environment { "extras": "", "marker": "extra == \"metal\"", "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`metalCoord; extra == "metal"`	runtime
molvs Environment { "extras": "", "marker": "extra == \"tautomer\"", "requires_python": ">=3.8", "evaluation": "NOT_EVALUATED" }	`molvs; extra == "tautomer"`	runtime