API Documentation

API Reference

• Solute
  • Solute
    • Solute.__init__()
    • Solute.from_atoms()
    • Solute.from_atoms_dict()
    • Solute.from_solute_list()
    • Solute.plot_solvation_radius()
    • Solute.draw_molecule()
    • Solute.get_shell()
    • Solute.get_closest_n_mol()
    • Solute.radial_shell()
• Coordination
  • Coordination
    • Coordination.__init__()
    • Coordination.from_solute()
    • Coordination.coordination_numbers
    • Coordination.coordination_numbers_by_frame
    • Coordination.coordinating_atoms
    • Coordination.coordination_vs_random
• Networking
  • Networking
    • Networking.__init__()
    • Networking.from_solute()
    • Networking.get_network_res_ix()
    • Networking.network_df
    • Networking.network_sizes
    • Networking.solute_status
    • Networking.solute_status_by_frame
• Pairing
  • Pairing
    • Pairing.__init__()
    • Pairing.from_solute()
    • Pairing.solvent_pairing
    • Pairing.pairing_by_frame
    • Pairing.fraction_free_solvents
    • Pairing.diluent_composition
    • Pairing.diluent_composition_by_frame
    • Pairing.diluent_counts
• Residence
  • Residence
    • Residence.__init__()
    • Residence.from_solute()
    • Residence.plot_auto_covariance()
    • Residence.auto_covariances
    • Residence.residence_times_cutoff
    • Residence.residence_times_fit
    • Residence.fit_parameters
• Speciation
  • Speciation
    • Speciation.__init__()
    • Speciation.from_solute()
    • Speciation.calculate_shell_fraction()
    • Speciation.get_shells()
    • Speciation.speciation_data
    • Speciation.speciation_fraction
    • Speciation.solvent_co_occurrence
• Plotting
  • plot_network_size_histogram()
  • plot_shell_composition_by_size()
  • plot_co_occurrence()
  • compare_solvent_dicts()
  • compare_pairing()
  • compare_free_solvents()
  • compare_diluent()
  • compare_coordination_numbers()
  • compare_residence_times_cutoff()
  • compare_residence_times_fit()