Documentation

• Packing Class
  • Packing
    • Packing.animate()
    • Packing.coordination()
    • Packing.generate()
    • Packing.initialize()
    • Packing.plot()
    • Packing.rotate()
    • Packing.save()
    • Packing.set_frame()
• Elastic Class
  • Elastic
    • Elastic.compute_modes()
    • Elastic.energy()
    • Elastic.mean_square_displacement()
    • Elastic.plot_network()
    • Elastic.reset_equilibrium()
    • Elastic.reset_init()
    • Elastic.reset_view()
    • Elastic.rigid_correction()
    • Elastic.rotate_view()
    • Elastic.save()
    • Elastic.set_axes()
    • Elastic.set_frame()
    • Elastic.solve()
• Allosteric Class
  • Allosteric
    • Allosteric.add_sources()
    • Allosteric.add_targets()
    • Allosteric.animate()
    • Allosteric.color_plot()
    • Allosteric.distribution_plot()
    • Allosteric.mode_plot()
    • Allosteric.mode_tile()
    • Allosteric.plot()
    • Allosteric.plot_source()
    • Allosteric.plot_target()
    • Allosteric.reset_equilibrium()
    • Allosteric.rotate()
    • Allosteric.save()
    • Allosteric.strain()
    • Allosteric.strain_map()
    • Allosteric.strain_plot()
    • Allosteric.strain_plot_thermal()
    • Allosteric.time_lapse()
    • Allosteric.write_job()
    • Allosteric.write_lammps_data()
    • Allosteric.write_lammps_data_learning()
    • Allosteric.write_lammps_input()
• LAMMPS helper modules
  • get_clusters()
  • load_run()
  • read_data()
  • read_dim()
  • read_dump()
  • read_log()
  • setup_run()