Introduction

clusttraj is a Python package which aims to cluster similar configurations of molecular dynamics or Monte Carlo simulation trajectories.

The optimal alignment between each snapshot is sought using reordering algorithms and optimal rotations.

Any format supported by openbabel is accepted as input or output, including the popular .xyz, .pdb and .xtc.

Motivation

The idea of clusttraj is to be an easy to use, and easy to extend platform for clustering trajectories.

We also focus in providing options for the analysis of solute-solvent systems.

Limitations

clusttraj is limited by the agglomerative clustering algorithms provided by SciPy.

However, there are many algorithms implemented for one to choose, as can be seen here.