molecule_rxn

Molecule_rxn is a python package used for generating possible intermediates from molecules in a recursive and brute-force way. SMILES notation can be generated from ASE trajectory file and graph representation. EC_fp enables customized invariants for atoms in Morgan Fingerprinting.

Installation

• Create conda environment and install RDkit: conda create -n molecule_rxn -c rdkit/label/beta rdkit python=3.6
• Activate conda environment: conda activate molecule_rxn
• Install dependencies:
  • imolecule: pip install imolecule
  • networkx: pip install networkx
  • ASE: pip install --upgrade --user ase
  • Open Babel: conda install -c conda-forge openbabel
  • bitarray: pip install bitarray
• Download molecule_rxn: git clone https://github.com/cchang373/molecule_rxn.git
• Installation: install the package with pip install -e molecule_rxn

Usage

Generation of intermediates and SMILES notation, graph representation

See example.py

Generation of surface species

from molecule_rxn.add_metal import add_metal, add_metal_all
species_single = add_metal().add_metal('[O]C[C]', 'Rh')
species_all = add_metal_all().add_metal_all(['[O]C[C]'], 'Rh')

Generation of modified Morgan Fingerprinting

from molecule_rxn.EC_fp.EC_fp import ecfp
from rdkit import Chem

mol = Chem.MolFromSmiles('CO')
bitInfo = ecfp(mol, 2) #Mol object, radius