RDKIT molecule

[silviamenin]

I'm currently working with fingerprints calculation in molecular dynamics trajectories.
To do this I need to convert protein and ligand in a pdb file for every single frame, and then reopen every file with oddt.toolkits.readfile(). It's a huge quantity of files and it's a very slow process, because every instance need to be opened 2 times.
I've tried to convert protein and ligand instances to rdkit molecule, but I'm not able to transform the rdkit_mol object to oddt_mol object.
How can I overcome this problem?
Thank you to those who will answer me.

[mwojcikowski]

You can construct oddt molecule using rdkit's Chem.Mol object instance when initiating. https://github.com/oddt/oddt/blob/master/oddt/toolkits/rdk.py#L389.

from oddt.toolkits.rdk import Molecule

rdkit_mol = Chem.MolFromSmiles('CCC')
oddt_mol = Molecule(rdkit_mol)