From 60ae4ce24400a5d5573d5986abedecdf599e3f5c Mon Sep 17 00:00:00 2001 From: Kevin Wu Date: Fri, 9 Sep 2022 14:09:32 -0700 Subject: [PATCH] README updates --- README.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/README.md b/README.md index b122a56..29ea245 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,8 @@ We present a diffusion model for generating novel protein backbone structures. ## Installation +This software is written in Python, notably using PyTorch, PyTorch Ligthing, and the HuggingFace +transformers library. The required conda environment is defined within the `environment.yml` file. To set this up, make sure you have conda (or mamba) installed and run: @@ -25,6 +27,17 @@ cd data # Ensure that you are in the data subdirectory within the codebase ./download_cath.sh ``` +## Sampling protein backbones + +To sample protein backbones, use the script `bin/sample.py`. An example command to do this is as follows. + +```bash +python ~/protdiff/bin/sample.py ../projects/models/full_angles/results/ --num 512 --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. + ## Tests Tests are implemented through a mixture of doctests and unittests. To run unittests, run: