Merging fragment and core using RDKit for FragPELE

frag_pele_rdkit.py

from rdkit.Chem import rdchem
from rdkit import Chem

# Import molecules
core = Chem.MolFromPDBFile('../FFF/core.pdb')
fragment = Chem.MolFromPDBFile('../FFF/fragment.pdb')

# Merge both molecules
combo = Chem.CombineMols(core,fragment)

# Convert merged molecule to RWmol si we can add a bond between the two molecules (now they're separated)                                                                             
mw = Chem.RWMol(combo)
mw.AddBond(11,5) # In this case, 11 and 5 are the atom idx from the rdkit mw molecule. 

# Convert RWMol to SMILES
Chem.MolToSmiles(mw)

# Sanitize to fix connectivity
Chem.SanitizeMol(mw)
smiles = Chem.MolToSmiles(mw)

# Convert back to mol so we can save into PDB
m = Chem.MolFromSmiles(smiles)

# Save merged molecule into a PDB file.
Chem.MolToPDBFile(m,'m.pdb')