molfunc
About
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. Possible use cases include catalyst functionalisation, ligand modification and combinatorial molecule generation.
Installation
If the requirements (rdkit, numpy, scipy, networkx) are already satisfied:
pip install molfunc
Otherwise, clone this repository and cd into the top level molfunc directory:
git clone https://github.com/duartegroup/molfunc.git
cd molfunc/
install the Python dependencies using conda (anaconda or miniconda) and install:
conda config --append channels conda-forge
conda install --file requirements.txt
python setup.py install
Usage
A minimal example to convert PH3 to PMe3
from molfunc import CoreMolecule, CombinedMolecule
ph3 = CoreMolecule(xyz_filename='examples/PH3.xyz', atoms_to_del=[2, 3, 4])
pme3 = CombinedMolecule(core_mol=ph3, frag_smiles='C[*]', name='PMe3')
pme3.print_xyz_file()molfunc can also be used from the command line
molfunc examples/PH3.xyz -a 2 3 4 -s C[*]
where in both cases all hydrogen atoms are swapped for methyls. See examples/ for more examples.