Protenij: Protein + X + J

Translation of Protenix to JAX/Equinox. This is pretty rough, we suggest using it through mosaic.

Installation

PyTorch is an optional dependency. The full inference pipeline (featurization, model loading, structure prediction) runs without it.

# Inference only (no PyTorch)
uv sync

# With PyTorch (needed for converting checkpoints from the original Protenix format)
uv sync --extra torch

Serialized models

Pre-converted Equinox models skip the PyTorch dependency entirely and load in under a second.

Model	Params	.eqx size
protenix_tiny_default_v0.5.0	110M	438 MB
protenix_mini_default_v0.5.0	134M	536 MB
protenix_base_default_v1.0.0	368M	1474 MB
protenix_base_20250630_v1.0.0	368M	1474 MB

Loading

Models are hosted on HuggingFace and downloaded automatically on first use.

from protenix.backend import load_model

# Downloads from HuggingFace, caches to ~/.protenix/
model = load_model("protenix_base_default_v1.0.0")

# Or load from an explicit path
model = load_model("~/.protenix/protenix_base_default_v1.0.0")

Translating from a PyTorch checkpoint

Requires the torch extra.

uv sync --extra torch
python translate_models.py

This downloads any missing checkpoints, converts each model to Equinox, saves .eqx + .skeleton.pkl to ~/.protenix/, and verifies a bit-exact round-trip.