Generated ligand poses are not in the protein pocket

I ran the sample.py script and from the pool.finished object I get a list of data. For each data I call reconstruct_from_generated to get out a rdkit molecule with a 3D conformation.

However, it seems the conformation is not in the same coordinate space as the protein pocket:

I sampled idx 50 and looked at the samples_all.pt file, the corresponding protein pocket I loaded is thus: FKB1A_HUMAN_2_108_0/1d7j_A_rec_1tco_fk5_lig_tt_docked_0_pocket10.pdb

I see the ligand (left) is far away from the pocket (right)

Am I doing something wrong?

[luost26]

for me, the sample.pt stored in the finished array a list of pytorch geometric data object which can be turned into rdkit molecule using the function reconstruct_from_generated

Sorry to bother you again, I do not know how to use the reconstruct_from_generated function to convert the ‘pt’ files to sdf conformation, could you please show me your code?

Hi, I have updated sample.py.

The generated molecules will be now saved as SDF files and SMILES files, beside the original .pt format.

[luost26]

Hi,

The PDB file of data#50 should be:

  protein_filename='IMA1_HUMAN_68_497_0/4u5s_A_rec_4u54_3c5_lig_tt_min_0_pocket10.pdb',
  ligand_filename='IMA1_HUMAN_68_497_0/4u5s_A_rec_4u54_3c5_lig_tt_min_0.sdf',
  id=93345,

You may get them by inserting print(data) into the sampling script.

The ordering of data in the testset is different from the ordering of test_set.tsv