Atomistic simulations generate large volumes of noisy structural data, yet extracting phase labels and continuous order parameters (OPs) in a robust and general manner remains challenging. Existing tools are often specialized to a limited set of prototypes and split thermal-noise removal, phase classification, and OP construction into separate steps. Here we present a unified probabilistic framework for analyzing noisy atomic configurations with respect to known crystal prototypes. The model predicts per-atom, per-prototype logits and aggregates them into a scalar log-probability (logP) landscape over atomic coordinates. Its gradient defines a conservative denoising field, while the logits provide local phase labels, prototype-resolved OPs, and ambiguity measures through logit margins. We train on AFLOW-mapped crystalline structures from the Materials Project with synthetic positional and elastic perturbations, then test extrapolation to stronger noise, finite-temperature disorder, point defects, water--ice coexistence, binary polymorphs, and shock-compressed Ti. A single differentiable scalar model recovers prototype identity after denoising, tracks smooth transformations such as Bain and Burgers paths, and exposes low-confidence regions near defects and phase boundaries. This provides an integrated and extensible tool for analyzing complex atomistic simulations.