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rdkit

RDKIT: Combine/Add particles

I have a database of macrocycles and covalent organic cages, where I wish to add a molecule/ion into the cavity. I need to do this through RDKIT. Is there an easy method to accomplish this task?

For example:

from rdkit import AllChem

guest = [x_value, y_value, z_value]
cage = AllChem.MolFromMolFile('cage_file.mol')

cage_guest = cage+guest (along the lines of)

I am then hoping to be able to manipulate the cage_guest in the usual fashion.

Solution

  • I do not think this is possible natively in rdkit. You should take a look at stk, which uses rdkit for building organic cages. Here seems to be the system you require.