acedrg

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.