Ligand connections and bond distances are not respected

[kweber1]

ligands.zip

It seems that my ligand is compressed and bonds are distorted after running generate_new.py (after changing it to my protein and ligand).

I attached the zip file with the original ligand as well as the outputs from the model.

I am using the checkpoint given in your GitHub for the weights.

My software versions:
https://pastebin.com/0cV7Re9u

My console output:

[zaixizhang]

Thanks for your feedback! Will try to reproduce and correct the outputs for your ligands.

[DS-ribo]

Hi Zaixi,

Thank you for the code - I was wondering if there was a follow up on this problem?

Best,
Daniel

[zaixizhang]

Hi Daniel, I was trying to reproduce the problem. I realized the original protein was not shared in the ligands.zip. In your case, could relax_sdf fix the connections/distances?

PocketGen/utils/relax.py

Line 83 in 81e14bf

def relax_sdf(sdf):