Closed orgw closed 1 year ago
Hi @orgw!
To sample linkers conditioned on protein pockets you can repeat the same procedure as explained in section Sampling but using different datasets and models:
First, download test dataset:
mkdir -p datasets
wget https://zenodo.org/record/7121280/files/MOAD_test_bb.pt?download=1 -O datasets/MOAD_test_bb.pt
Download the necessary model:
mkdir -p models
wget https://zenodo.org/record/7121300/files/pockets_difflinker_backbone.ckpt?download=1 -O models/pockets_difflinker_backbone.ckpt
Next, create necessary directories:
mkdir -p samples
mkdir -p trajectories
And sample:
python -W ignore sample.py \
--checkpoint models/pockets_difflinker_backbone.ckpt \
--samples samples \
--data datasets \
--prefix MOAD_test_bb \
--n_samples 2 \
--device cuda:0
Please let me know if you have other questions!
P.S. I found a bug while was running the commands above so thank you for asking!
Thank you! As you've said there was a problem so I've mentioned it
Hi,
How do you sample with protein??
thanks