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