PyTraj

PyTraj, commonly written pytraj, is a Python library that exposes a high-level API to the cpptraj trajectory analysis engine. It is part of the AmberTools software package and provides Python bindings for performing routine and advanced analyses on molecular dynamics trajectories.

PyTraj implements a Pythonic interface around cpptraj commands, enabling users to load trajectories and topologies, slice data, and perform analyses without writing C++ code. It supports common MD trajectory formats and can read data produced by widely used simulation workflows. Analyses include RMSD and RMSF, distances, hydrogen bonds, dihedrals and angles, radial distribution functions, clustering, principal component analysis, and secondary-structure assessment.

Usage typically involves loading a topology and trajectory, applying a sequence of selections and analysis commands, and retrieving results as Python objects suitable for further processing with NumPy or plotting libraries.

PyTraj is distributed as part of AmberTools and is open source. It can be installed via conda-forge or PyPI and requires a compatible cpptraj installation. The project is maintained by the Amber MD community and related developers, with ongoing additions to analysis functionality.