Installation

Setup a Python environment

To ensure a clean and isolated setup, we recommend to use uv, a lightweight tool that simplifies Python environment and package management. If you don’t have it yet:

macOS / LinuxWindows

curl -LsSf https://astral.sh/uv/install.sh | sh

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
$env:Path += ";$env:USERPROFILE\.local\bin"

Create and activate a virtual environment with uv:

macOS / LinuxWindows

uv venv
source .venv/bin/activate

uv venv
.venv\Scripts\activate

Tip

Using uv helps manage dependencies easily and keeps your environment clean, avoiding conflicts with other Python packages.

Install WILDkCAT from PyPI

Install WILDkCAT directly from PyPI:

uv pip install wildkcat

Verify the installation by checking the version:

wildkcat --version

Environment Setup

Provide your BRENDA login credentials and Entrez API email adress to query the BRENDA enzyme database and NCBI database.

Create a file named .env in the root of your project with the following content:

ENTREZ_EMAIL=your_email@example.com
BRENDA_EMAIL=your_email@example.com
BRENDA_PASSWORD=your_password

Note

Replace the placeholders with the credentials from the BRENDA website account you created.

Danger

Keep the file .env private (e.g., add it to your .gitignore) as it contains sensitive information.

Install CataPro

CataPro is required for predicting kcat values using machine learning

1. Install dependencies

uv pip install torch transformers numpy pandas RDKit sentencepiece

2. Clone the CataPro repository

git clone https://github.com/zchwang/CataPro

3. Set up Git LFS

CataPro uses Git Large File Storage (LFS) to handle large model files. If you don't have Git LFS installed, you can install it using the following command:

git lfs install

4. Download the models

CataPro requires the models ProtT5 model and MolT5 model.

Warning

The models prot_t5_xl_uniref50 and molt5-base-smiles2caption required for CataPro are 64 and 1.9 GB, respectively.

macOS / LinuxWindows

cd CataPro/models/

LFS_SKIP_SMUDGE=1 git clone https://huggingface.co/Rostlab/prot_t5_xl_uniref50
cd prot_t5_xl_uniref50
git lfs pull

cd ..

LFS_SKIP_SMUDGE=1 git clone https://huggingface.co/laituan245/molt5-base-smiles2caption
cd molt5-base-smiles2caption
git lfs pull

cd ../..

git -c filter.lfs.smudge= -c filter.lfs.required=false clone https://huggingface.co/Rostlab/prot_t5_xl_uniref50
cd prot_t5_xl_uniref50
git lfs pull

cd ..

git -c filter.lfs.smudge= -c filter.lfs.required=false clone https://huggingface.co/laituan245/molt5-base-smiles2caption
cd molt5-base-smiles2caption
git lfs pull

cd ../..