pallatom

pallatom is a protein structure diffusion model implementing EDM-based denoising over atomic coordinates, built on AlphaFold 3–style architecture components.

Architecture

API Reference

Overview

The library is divided into four subpackages:

Package

Description

pallatom.architecture

Core neural network modules — MainTrunk, attention blocks, pair updates, template embedder, and loss functions.

pallatom.helpers

Data loading (ProteinDataset), featurization (Distogram, ProteinBatch), Kabsch alignment, and atom/residue constants.

pallatom.train

Pydantic training configuration (TrainingParams, ModelParams, NoiseScheduleParams, …) and the training/evaluation loop.

pallatom.sample

Pydantic sampling configuration and EDMPrecond — the EDM-compatible denoiser wrapper for inference.

Indices