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arneschneuing / DiffSBDD

A Euclidean diffusion model for structure-based drug design.
MIT License
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How to sample mols on all pockets of the test set of Crossdocked dataset? #25

Open mathfirst opened 1 year ago

mathfirst commented 1 year ago

Hi, I am trying to set DiffSBDD cond method as one of baselines in my work, I would like to sample mols given 100 pockets from the test set of Crossdocked dataset on my own machine. What can I do?

python generate_ligands.py <checkpoint>.ckpt --pdbfile <pdb_file>.pdb --outdir <output_dir> --resi_list <list_of_pocket_residue_ids>

How can I specify --resi_list or --ref_ligand :?

Does the following command only work for the Bindingmoad dataset? I only need to run your sample code on the test set of Crossdoced.

python test.py <checkpoint>.ckpt --test_dir <bindingmoad_dir>/processed_noH/test/ --outdir <output_dir> --fix_n_nodes

Could you please give me some instructions for my goal?

mathfirst commented 1 year ago

In addition, I have preprocessed the CrossDocked dataset in the same way as Pocket2Mol.

yuanqidu commented 1 year ago

Thanks for your interest in our work.

The following command would work for crossdocked dataset as well for sampling over the test set

python test.py <checkpoint>.ckpt --test_dir <bindingmoad_dir>/processed_noH/test/ --outdir <output_dir> --fix_n_nodes

mathfirst commented 1 year ago

Thanks! I'm using generate_ligands.py with a for-loop to do that. It works now.

arneschneuing commented 1 year ago

Hi, I would just like to add that this repository only contains checkpoints for BindingMOAD at the moment. Please keep this in mind when sampling molecules for the CrossDocked test set.

mathfirst commented 1 year ago

Where can I get the checkpoint for the CrossDocked dataset? Can you upload it here?

mathfirst commented 1 year ago

Hi, I would just like to add that this repository only contains checkpoints for BindingMOAD at the moment. Please keep this in mind when sampling molecules for the CrossDocked test set.

The following checkpoint

https://github.com/arneschneuing/DiffSBDD/blob/main/checkpoints/full_atom.ckpt

is only for BindingMOAD? However, I am using it to sample molecules for the CrossDocked test set right now.

arneschneuing commented 1 year ago

Yes, the model was trained on the Binding MOAD dataset