Issue with Vina Docking During Molecule Evaluation

[mahmoud-ekhani]

Firstly, I would like to express my gratitude for your impressive work and for making it available on GitHub.

I recently utilized your pre-trained model to generate molecules for a specific pocket using the following command: python scripts/sample_for_pocket.py configs/sampling.yml --pdb_path examples/1zcm.pdb. However, I encountered an issue when it came to the vina docking step during evaluation by scripts/evaluate_diffusion.py . Specifically, the 'ligand_filename': r['data'].ligand_filename, does not appear to exist in the results generated by sample_for_pocket.py.

In order to resolve this issue, I removed the aforementioned snippet from lines 110 and 143 in the scripts/evaluate_diffusion.py code. Post this modification, the problem seems to be resolved. I am raising this issue to bring this to your attention, and potentially help others who might encounter a similar problem.