molfunc is a Python tool for functionalisation of 3D molecules. Given a .xyz file molecular functionalisation is performed by specifying monovalent atoms in the structure to swap for a set of fragments given as their corresponding SMILES strings. The energy of the combined molecule is minimised with purely rigid body rotations, as such, generated structures may require further (constrained) optimisation. Possible use cases include catalyst functionalisation, ligand modification and combinatorial molecule generation.
pip install molfunc==2.0.0b0
The old Python/Cython version is still available with pip install molfunc=1.0.0. Alternatively, to install from source:
git clone https://github.com/duartegroup/molfunc.git
cd molfunc/
pip install Cython
python setup.py install
NOTE: Requires a modern C++ compiler.
molfunc provides a minimal Python API and core CLI. To convert PH3 to PMe3 in Python:
from molfunc import print_combined_molecule
print_combined_molecule(core_xyz_filename='examples/PH3.xyz',
atoms_to_del=[2, 3, 4],
frag_names=['Me'],
name='PMe3')or from the command line:
molfunc examples/PH3.xyz -a 2 3 4 -f Me
where in both cases all hydrogen atoms (atom indexes 2, 3, 4) are swapped for methyls. See examples/ for more examples. Functionalising with all combinations of fragments is also possible with
molfunc examples/PH3.xyz -a 2 --all
If molfunc us used in a publication please consider citing the autodE paper where it's outlined:
T. A. Young, J. J. Silcock, A. J. Sterling, F. Duarte, Angew. Chem. Int. Ed., 2021, 60, 4266.