ME 5329 Assignment 0

Assignment 0

Code Block in Instructions

generate_structure.py

from rdkit import Chem
from rdkit.Chem import AllChem
import os

smile_string = "CCCC"
filename = "butane.xyz"

rdkit_mol = Chem.AddHs(Chem.MolFromSmiles(smile_string))
AllChem.EmbedMolecule(rdkit_mol)
AllChem.MMFFOptimizeMolecule(rdkit_mol)
filepath = os.path.join(os.getcwd(), filename)
Chem.MolToXYZFile(rdkit_mol, filepath)