molPX: Molecular Projection Explorer

molPX is an Ipython module that provides, within a Jupyter notebook, interactive molecular visualization of virtually any type of coordinate that a molecular dynamics (MD) trajectory has been projected to. From the more intuitive coordinates, such as distances, contacts, angles etc, to the less intuitive projections such as principal components (PCs), time-independent components (TICs) or any collective variable or order parameter that was used to analyze the MD data.

molPX interactively connects a visual representation of the molecule (via NGLview) to other types of graphs such as:

  • free energy surfaces
  • trajectories as f(t)
  • Markov-State-Models
  • transition pathways

and virtually any (plottable) type of MD-associated information that the user has generated outside or inside the Jupyter notebook.