Note:

Code maintained now at https://github.com/automl/RNAinformer/

RNAinformer

This repository contains the source code to RNAinformer: Generative RNA Design with Tertiary Interactions.

Download the repository and extract it.

cd RNA-design

Install virtual environment

conda env create -f environment.yml

conda activate rnadesign

The Flash Attention package currently requires an Ampere, Ada, or Hopper GPU (e.g., A100, RTX 3090, RTX 4090, H100). To install Falsh-attn.

pip install -U --no-cache-dir flash-attn==2.3.4

Datasets

To get the training and test sets download and unzip data from https://www.dropbox.com/scl/fi/yaxvlsloht21i7bho2tim/data.tar.xz?rlkey=jmxqbjjcmbumt08hk2tbqxvgg&st=k9jfe7iz&dl=0

wget -O data.tar.xz https://www.dropbox.com/scl/fi/yaxvlsloht21i7bho2tim/data.tar.xz?rlkey=j
mxqbjjcmbumt08hk2tbqxvgg&st=k9jfe7iz&dl=0
tar -xvf data.tar.xz
rm data.tar.xz

Models and predictions

To get the models and designed predictions download and unzip data from https://www.dropbox.com/scl/fi/4ti5cn1zuct5u37rzkpod/runs.tar.xz?rlkey=jfu6trrvnr9d118mrsecgquzp&st=eccnnqy8&dl=0

wget -O runs.tar.xz https://www.dropbox.com/scl/fi/4ti5cn1zuct5u37rzkpod/runs.tar.xz?rlkey=jfu6tr
rvnr9d118mrsecgquzp&st=eccnnqy8&dl=0
tar -xvf runs.tar.xz
rm runs.tar.xz

Evaluate

Evaluation metrics have been provided for all model and competitors in respective metrics.csv files To run all evaluations again

bash run_evaluation.sh

Inference on test sets

python inference.py --seed 9647359 --path path/to/model/folder/

Eg.

python inference.py --seed 9647359 --path runs/syn_pdb/version_0/

Use --flash False if Flash attention is not installed

python inference.py --seed 9647359 --path runs/syn_pdb/version_0/ --flash False