DiffDock
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gcorso
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
Hi, I followed the readme to install the DiffDock-L as follows: conda env create --file environment.yml conda activate diffdock However, when I tried running the "interface" python I faced the...
After creating environment and all the dependencies the final command line python3 -m inference.py --config default_inference_args.yaml --protein_ligand_csv data/protein_ligand_example_csv.csv --out_dir results/user_predictions_small give error terminate called after throwing an instance of 'std::bad_alloc'...
# My error ## Generate the ESM2 embeddings for the proteins: ```python python datasets/esm_embedding_preparation.py ``` I downloaded the BindingMOAD dataset and extracted it into the "/data/BindingMOAD_2020_ab_processed_biounit" directory. I ran "datasets/esm_embedding_preparation.py",...
Hi, I am running this as the example: python -m inference --config default_inference_args.yaml --protein_ligand_csv data/protein_ligand_example.csv --out_dir results/ Before I was able to run it completely but I reinstalled the things...
Hello Team, I have some trouble with following the dataset loader for the Moad dataset. This [line](https://github.com/gcorso/DiffDock/blob/main/datasets/moad.py#L466) suggests that there should be a directory `pdb_ligand` in the moad archive. I...
I tried to retrain the model with the PDBBind dataset, I ran the train.py script directly without any parameter, and it finished the whole training process very quickly (
Hi, I am having issues installing openfold. I have followed the install instructions included on the README thus far. I think the error I am getting is arising due to...
I'm testing a dataset of ligands against the same protein. Instead of loading the same protein pdb file everytime, is there anyway to load the pdb once, and just start...
python -m inference --config default_inference_args.yaml --protein_path ./rec_1.pdb --ligand ./ZINC01535869.mol2 --out_dir ./outache/ --inference_steps 20 --samples_per_complex 40 --batch_size 10 --actual_steps 18 --no_final_step_noise The following error occurred and there was no output. Does...
Hi, I observed while running the command [ time python -m inference --config default_inference_args.yaml --protein_ligand_csv data/test_1.csv --out_dir results_L_cpu/user_predictions_small] the GPU memory is used while the device is changed to 'cpu'...
