boltzkit.utils.molecular.plot_molecule

Functions

plot_matplotlib_molecule(topology, positions)

Plots an OpenMM molecule using Matplotlib 3D.
boltzkit.utils.molecular.plot_molecule.plot_matplotlib_molecule(topology, positions, figsize=(4, 4), atom_scale=50)[source]

Plots an OpenMM molecule using Matplotlib 3D. While not being visually the best, it provides a simple and reliable way to inspect molecular structures (e.g., for debugging).

Parameters:

  • topology (openmm.app.Topology) – OpenMM topology object

  • positions (openmm.unit.Quantity or numpy.ndarray) – Atomic positions in nanometers

  • figsize (tuple) – Figure size

  • atom_scale (float) – Scale factor for atom size