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Kevin Wu
2022-09-09 14:09:32 -07:00
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README.md
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@@ -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: