waterEntropy package

Subpackages

• waterEntropy.analysis package
  • Submodules
  • waterEntropy.analysis.HB module
    • HBCollection
      • HBCollection.__dict__
      • HBCollection.__firstlineno__
      • HBCollection.__init__()
      • HBCollection.__module__
      • HBCollection.__static_attributes__
      • HBCollection.__weakref__
      • HBCollection.add_data()
      • HBCollection.find_acceptor()
      • HBCollection.find_donators()
    • get_HB_terms()
    • get_shell_HB_acceptors()
    • get_shell_HBs()
  • waterEntropy.analysis.HB_labels module
    • HBLabelCollection
      • HBLabelCollection.__dict__
      • HBLabelCollection.__firstlineno__
      • HBLabelCollection.__init__()
      • HBLabelCollection.__module__
      • HBLabelCollection.__static_attributes__
      • HBLabelCollection.__weakref__
      • HBLabelCollection.add_accepts_from()
      • HBLabelCollection.add_data()
      • HBLabelCollection.add_donates_to()
      • HBLabelCollection.add_shell_counts()
      • HBLabelCollection.merge()
    • get_HB_labels()
  • waterEntropy.analysis.RAD module
    • get_RAD_neighbours()
    • get_RAD_shell()
  • waterEntropy.analysis.shell_labels module
    • get_nearest_nonlike()
    • get_shell_labels()
  • waterEntropy.analysis.shells module
    • Shell
      • Shell.__dict__
      • Shell.__firstlineno__
      • Shell.__getattr__()
      • Shell.__init__()
      • Shell.__module__
      • Shell.__repr__()
      • Shell.__setattr__()
      • Shell.__static_attributes__
      • Shell.__weakref__
    • ShellCollection
      • ShellCollection.__dict__
      • ShellCollection.__firstlineno__
      • ShellCollection.__init__()
      • ShellCollection.__module__
      • ShellCollection.__repr__()
      • ShellCollection.__static_attributes__
      • ShellCollection.__weakref__
      • ShellCollection.add_data()
      • ShellCollection.find_shell()
      • ShellCollection.set_property()
  • Module contents
• waterEntropy.entropy package
  • Submodules
  • waterEntropy.entropy.convariances module
    • CovarianceCollection
      • CovarianceCollection.__dict__
      • CovarianceCollection.__firstlineno__
      • CovarianceCollection.__init__()
      • CovarianceCollection.__module__
      • CovarianceCollection.__static_attributes__
      • CovarianceCollection.__weakref__
      • CovarianceCollection.add_data()
      • CovarianceCollection.merge()
      • CovarianceCollection.populate_dicts()
      • CovarianceCollection.update_counts()
  • waterEntropy.entropy.orientations module
    • Orientations
      • Orientations.__dict__
      • Orientations.__firstlineno__
      • Orientations.__init__()
      • Orientations.__module__
      • Orientations.__static_attributes__
      • Orientations.__weakref__
      • Orientations.add_data()
      • Orientations.get_orientational_entropy_from_dict()
      • Orientations.get_resid_orientational_entropy_from_dict()
      • Orientations.get_running_average()
    • WaterOrientCalculator
      • WaterOrientCalculator.GAS_CONSTANT
      • WaterOrientCalculator.__dict__
      • WaterOrientCalculator.__firstlineno__
      • WaterOrientCalculator.__init__()
      • WaterOrientCalculator.__module__
      • WaterOrientCalculator.__static_attributes__
      • WaterOrientCalculator.__weakref__
      • WaterOrientCalculator.add_data()
      • WaterOrientCalculator.get_donor_acceptor_probabilities()
      • WaterOrientCalculator.get_hb_probability()
      • WaterOrientCalculator.get_non_HB_data()
      • WaterOrientCalculator.get_orientation_S()
      • WaterOrientCalculator.get_reduced_neighbours_biases()
      • WaterOrientCalculator.get_shell_degeneracy()
    • print_Sorient_dicts()
  • waterEntropy.entropy.vibrations module
    • Vibrations
      • Vibrations.ANGSTROM_TO_METRE
      • Vibrations.AVOGADRO
      • Vibrations.BOLTZMANN
      • Vibrations.CALORIE_TO_JOULE
      • Vibrations.GAS_CONSTANT
      • Vibrations.HBAR
      • Vibrations.KG_TO_AMU
      • Vibrations.KJ_TO_J
      • Vibrations.NANOMETRE_TO_METRE
      • Vibrations.PER_MOLE_TO_PER_MOLECULE
      • Vibrations.__dict__
      • Vibrations.__firstlineno__
      • Vibrations.__init__()
      • Vibrations.__module__
      • Vibrations.__static_attributes__
      • Vibrations.__weakref__
      • Vibrations.add_data()
      • Vibrations.calculate_entropies()
      • Vibrations.calculate_frequencies()
      • Vibrations.get_data()
      • Vibrations.kJ_conversion()
      • Vibrations.kcal_conversion()
      • Vibrations.mda_conversion()
      • Vibrations.populate_dicts()
    • print_Svib_data()
  • Module contents
• waterEntropy.maths package
  • Submodules
  • waterEntropy.maths.transformations module
    • MOI()
    • get_UA_masses()
    • get_axes()
    • get_bonded_axes()
    • get_covariance_matrix()
    • get_custom_PI_MOI()
    • get_custom_axes()
    • get_flipped_axes()
    • get_mass_weighted_forces()
    • get_rotated_sum_forces()
    • get_torques()
  • waterEntropy.maths.trig module
    • get_angle()
    • get_distance()
    • get_neighbourlist()
    • get_shell_neighbour_selection()
    • get_sorted_neighbours()
    • get_vector()
  • Module contents
• waterEntropy.recipes package
  • Submodules
  • waterEntropy.recipes.bulk_water module
    • get_bulk_water_orient_entropy()
  • waterEntropy.recipes.forces_torques module
    • get_forces_torques()
  • waterEntropy.recipes.interfacial_solvent module
    • _entropy_per_step()
    • find_interfacial_solvent()
    • get_interfacial_shells()
    • get_interfacial_water_orient_entropy()
    • print_frame_solvent_dicts()
    • print_frame_solvent_shells()
    • save_solvent_indices()
    • save_solvent_shells()
  • Module contents
• waterEntropy.utils package
  • Submodules
  • waterEntropy.utils.dask_clusters module
    • check_slurm_env()
    • slurm_configure_cluster()
    • slurm_directives()
    • slurm_prologues()
    • slurm_submit_master()
    • system_network_interface()
  • waterEntropy.utils.helpers module
    • nested_dict()
  • waterEntropy.utils.selections module
    • find_bonded_atoms()
    • find_bonded_heavy_atom()
    • find_molecule_UAs()
    • find_solute_molecules()
    • get_selection()
    • guess_length_scale()
  • Module contents

Module contents

calculate water entropy near heterogeneous interfaces