From e54595fb474274e104a7b3bfee2ed1adb8e443c0 Mon Sep 17 00:00:00 2001 From: Kevin Wu Date: Mon, 26 Sep 2022 13:39:12 -0700 Subject: [PATCH] More example commands --- README.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 775d9ac..90a507c 100644 --- a/README.md +++ b/README.md @@ -60,14 +60,16 @@ cd data # Ensure that you are in the data subdirectory within the codebase ## Sampling protein backbones -To sample protein backbones, use the script `bin/sample.py`. An example command to do this using the pretrained weights described above is as follows. +To sample protein backbones, use the script `bin/sample.py`. Example commands to do this using the pretrained weights described above is as follows. ```bash +# To sample 256 backbones python ~/projects/protdiff/bin/sample.py ~/projects/protdiff/models/cath_pretrained --num 256 --device cuda:3 +# To sample 10 backbones per length ranging from [50, 128) - this reproduces results in our manuscript +python ~/projects/protdiff/bin/sample.py ~/projects/protdiff/models/cath_pretrained -l sweep --device cuda:3 ``` -This will run the model contained in the `results` folder and generate 512 sequences of varying lengths. -Not specifying a device will default to the first device `cuda:0`; use `--device cpu` to run on CPU. This will create the following directory structure in the diretory where it is run: +This will run the model contained in the `results` folder and generate 512 sequences of varying lengths. Not specifying a device will default to the first device `cuda:0`; use `--device cpu` to run on CPU. This will create the following directory structure in the diretory where it is run: ``` some_dir/