AceDRG generates stereochemical descriptions (restraint dictionaries) for ligands and links, for use in macromolecular refinement.
pip install acedrgPrebuilt 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 molvsacedrg -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 listThe 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.
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.
pip install ".[tautomer]" pytest
pytest -v python-tests --run-extraLong 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
Fei Long, Robert A. Nicholls, Paul Emsley, Saulius Gražulis, Andrius Merkys, Antanas Vaitkus, Garib N. Murshudov
Jordan Dialpuri, Lucrezia Catapano, Paul Emsley
- 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.