Quick Start

Quick Start#

This guide will get you started with PrxteinMPNN in just a few minutes.

Installation#

Install PrxteinMPNN using pip:

pip install -e .

Basic Usage#

Here’s a simple example to get you started:

import jax
import jax.numpy as jnp

from prxteinmpnn.mpnn import ProteinMPNNModelVersion, ModelWeights, get_mpnn_model
from prxteinmpnn.io import from_structure_file

# Load a protein structure
protein_structure = from_structure_file(filename="path/to/structure.pdb")

# Get the MPNN model
model = get_mpnn_model(
    model_version=ProteinMPNNModelVersion.V_48_020,
    model_weights=ModelWeights.DEFAULT
)

# Get the model inputs for the given structure
model_inputs = protein_structure_to_model_inputs(protein_structure)

# Score sequences
from prxteinmpnn.scoring.score import make_score_sequence
from prxteinmpnn.utils.decoding_order import random_decoding_order
key = jax.random.PRNGKey(0)  # Random key for JAX operations
score_sequence = make_score_sequence(parameters, random_decoding_order, model_inputs=model_inputs)
original_sequence_score, original_sequence_logits, original_decoding_order_used =
  score_sequence(
    key,
    inputs.sequence
  )
other_sequence = "SOMEOTHERSEQUENCE"
other_sequence_score, other_sequence_logits, new_decoding_order = score_sequence(
  key,
  other_sequence
)

Next Steps#

Contents