Index

_

__dict__ (waterEntropy.analysis.HB.HBCollection attribute) (waterEntropy.analysis.HB_labels.HBLabelCollection attribute) (waterEntropy.analysis.shells.Shell attribute) (waterEntropy.analysis.shells.ShellCollection attribute) (waterEntropy.entropy.convariances.CovarianceCollection attribute) (waterEntropy.entropy.orientations.Orientations attribute) (waterEntropy.entropy.orientations.WaterOrientCalculator attribute) (waterEntropy.entropy.vibrations.Vibrations attribute) __firstlineno__ (waterEntropy.analysis.HB.HBCollection attribute) (waterEntropy.analysis.HB_labels.HBLabelCollection attribute) (waterEntropy.analysis.shells.Shell attribute) (waterEntropy.analysis.shells.ShellCollection attribute) (waterEntropy.entropy.convariances.CovarianceCollection attribute) (waterEntropy.entropy.orientations.Orientations attribute) (waterEntropy.entropy.orientations.WaterOrientCalculator attribute) (waterEntropy.entropy.vibrations.Vibrations attribute) __getattr__() (waterEntropy.analysis.shells.Shell method) __init__() (waterEntropy.analysis.HB.HBCollection method) (waterEntropy.analysis.HB_labels.HBLabelCollection method) (waterEntropy.analysis.shells.Shell method) (waterEntropy.analysis.shells.ShellCollection method) (waterEntropy.entropy.convariances.CovarianceCollection method) (waterEntropy.entropy.orientations.Orientations method) (waterEntropy.entropy.orientations.WaterOrientCalculator method) (waterEntropy.entropy.vibrations.Vibrations method) __module__ (waterEntropy.analysis.HB.HBCollection attribute) (waterEntropy.analysis.HB_labels.HBLabelCollection attribute) (waterEntropy.analysis.shells.Shell attribute) (waterEntropy.analysis.shells.ShellCollection attribute) (waterEntropy.entropy.convariances.CovarianceCollection attribute) (waterEntropy.entropy.orientations.Orientations attribute) (waterEntropy.entropy.orientations.WaterOrientCalculator attribute) (waterEntropy.entropy.vibrations.Vibrations attribute)

__repr__() (waterEntropy.analysis.shells.Shell method) (waterEntropy.analysis.shells.ShellCollection method) __setattr__() (waterEntropy.analysis.shells.Shell method) __static_attributes__ (waterEntropy.analysis.HB.HBCollection attribute) (waterEntropy.analysis.HB_labels.HBLabelCollection attribute) (waterEntropy.analysis.shells.Shell attribute) (waterEntropy.analysis.shells.ShellCollection attribute) (waterEntropy.entropy.convariances.CovarianceCollection attribute) (waterEntropy.entropy.orientations.Orientations attribute) (waterEntropy.entropy.orientations.WaterOrientCalculator attribute) (waterEntropy.entropy.vibrations.Vibrations attribute) __weakref__ (waterEntropy.analysis.HB.HBCollection attribute) (waterEntropy.analysis.HB_labels.HBLabelCollection attribute) (waterEntropy.analysis.shells.Shell attribute) (waterEntropy.analysis.shells.ShellCollection attribute) (waterEntropy.entropy.convariances.CovarianceCollection attribute) (waterEntropy.entropy.orientations.Orientations attribute) (waterEntropy.entropy.orientations.WaterOrientCalculator attribute) (waterEntropy.entropy.vibrations.Vibrations attribute) _entropy_per_step() (in module waterEntropy.recipes.interfacial_solvent)

A

add_accepts_from() (waterEntropy.analysis.HB_labels.HBLabelCollection method) add_data() (waterEntropy.analysis.HB.HBCollection method) (waterEntropy.analysis.HB_labels.HBLabelCollection method) (waterEntropy.analysis.shells.ShellCollection method) (waterEntropy.entropy.convariances.CovarianceCollection method) (waterEntropy.entropy.orientations.Orientations method) (waterEntropy.entropy.orientations.WaterOrientCalculator method) (waterEntropy.entropy.vibrations.Vibrations method)

add_donates_to() (waterEntropy.analysis.HB_labels.HBLabelCollection method) add_shell_counts() (waterEntropy.analysis.HB_labels.HBLabelCollection method) ANGSTROM_TO_METRE (waterEntropy.entropy.vibrations.Vibrations attribute) AVOGADRO (waterEntropy.entropy.vibrations.Vibrations attribute)

B

BOLTZMANN (waterEntropy.entropy.vibrations.Vibrations attribute)

C

calculate_entropies() (waterEntropy.entropy.vibrations.Vibrations method) calculate_frequencies() (waterEntropy.entropy.vibrations.Vibrations method)

CALORIE_TO_JOULE (waterEntropy.entropy.vibrations.Vibrations attribute) check_slurm_env() (in module waterEntropy.utils.dask_clusters) CovarianceCollection (class in waterEntropy.entropy.convariances)

F

find_acceptor() (waterEntropy.analysis.HB.HBCollection method) find_bonded_atoms() (in module waterEntropy.utils.selections) find_bonded_heavy_atom() (in module waterEntropy.utils.selections) find_donators() (waterEntropy.analysis.HB.HBCollection method)

find_interfacial_solvent() (in module waterEntropy.recipes.interfacial_solvent) find_molecule_UAs() (in module waterEntropy.utils.selections) find_shell() (waterEntropy.analysis.shells.ShellCollection method) find_solute_molecules() (in module waterEntropy.utils.selections)

G

GAS_CONSTANT (waterEntropy.entropy.orientations.WaterOrientCalculator attribute) (waterEntropy.entropy.vibrations.Vibrations attribute) get_angle() (in module waterEntropy.maths.trig) get_axes() (in module waterEntropy.maths.transformations) get_bonded_axes() (in module waterEntropy.maths.transformations) get_bulk_water_orient_entropy() (in module waterEntropy.recipes.bulk_water) get_covariance_matrix() (in module waterEntropy.maths.transformations) get_custom_axes() (in module waterEntropy.maths.transformations) get_custom_PI_MOI() (in module waterEntropy.maths.transformations) get_data() (waterEntropy.entropy.vibrations.Vibrations method) get_distance() (in module waterEntropy.maths.trig) get_donor_acceptor_probabilities() (waterEntropy.entropy.orientations.WaterOrientCalculator method) get_flipped_axes() (in module waterEntropy.maths.transformations) get_forces_torques() (in module waterEntropy.recipes.forces_torques) get_HB_labels() (in module waterEntropy.analysis.HB_labels) get_hb_probability() (waterEntropy.entropy.orientations.WaterOrientCalculator method) get_HB_terms() (in module waterEntropy.analysis.HB) get_interfacial_shells() (in module waterEntropy.recipes.interfacial_solvent) get_interfacial_water_orient_entropy() (in module waterEntropy.recipes.interfacial_solvent) get_mass_weighted_forces() (in module waterEntropy.maths.transformations) get_nearest_nonlike() (in module waterEntropy.analysis.shell_labels)

get_neighbourlist() (in module waterEntropy.maths.trig) get_non_HB_data() (waterEntropy.entropy.orientations.WaterOrientCalculator method) get_orientation_S() (waterEntropy.entropy.orientations.WaterOrientCalculator method) get_orientational_entropy_from_dict() (waterEntropy.entropy.orientations.Orientations method) get_RAD_neighbours() (in module waterEntropy.analysis.RAD) get_RAD_shell() (in module waterEntropy.analysis.RAD) get_reduced_neighbours_biases() (waterEntropy.entropy.orientations.WaterOrientCalculator method) get_resid_orientational_entropy_from_dict() (waterEntropy.entropy.orientations.Orientations method) get_rotated_sum_forces() (in module waterEntropy.maths.transformations) get_running_average() (waterEntropy.entropy.orientations.Orientations method) get_selection() (in module waterEntropy.utils.selections) get_shell_degeneracy() (waterEntropy.entropy.orientations.WaterOrientCalculator method) get_shell_HB_acceptors() (in module waterEntropy.analysis.HB) get_shell_HBs() (in module waterEntropy.analysis.HB) get_shell_labels() (in module waterEntropy.analysis.shell_labels) get_shell_neighbour_selection() (in module waterEntropy.maths.trig) get_sorted_neighbours() (in module waterEntropy.maths.trig) get_torques() (in module waterEntropy.maths.transformations) get_UA_masses() (in module waterEntropy.maths.transformations) get_vector() (in module waterEntropy.maths.trig) guess_length_scale() (in module waterEntropy.utils.selections)

H

HBAR (waterEntropy.entropy.vibrations.Vibrations attribute)

HBCollection (class in waterEntropy.analysis.HB) HBLabelCollection (class in waterEntropy.analysis.HB_labels)

K

kcal_conversion() (waterEntropy.entropy.vibrations.Vibrations method) KG_TO_AMU (waterEntropy.entropy.vibrations.Vibrations attribute)

kJ_conversion() (waterEntropy.entropy.vibrations.Vibrations method) KJ_TO_J (waterEntropy.entropy.vibrations.Vibrations attribute)

M

mda_conversion() (waterEntropy.entropy.vibrations.Vibrations method) merge() (waterEntropy.analysis.HB_labels.HBLabelCollection method) (waterEntropy.entropy.convariances.CovarianceCollection method) module waterEntropy waterEntropy.analysis waterEntropy.analysis.HB waterEntropy.analysis.HB_labels waterEntropy.analysis.RAD waterEntropy.analysis.shell_labels waterEntropy.analysis.shells waterEntropy.entropy waterEntropy.entropy.convariances waterEntropy.entropy.orientations waterEntropy.entropy.vibrations waterEntropy.maths waterEntropy.maths.transformations waterEntropy.maths.trig waterEntropy.recipes waterEntropy.recipes.bulk_water waterEntropy.recipes.forces_torques waterEntropy.recipes.interfacial_solvent waterEntropy.utils waterEntropy.utils.dask_clusters waterEntropy.utils.helpers waterEntropy.utils.selections

MOI() (in module waterEntropy.maths.transformations)

N

NANOMETRE_TO_METRE (waterEntropy.entropy.vibrations.Vibrations attribute)

nested_dict() (in module waterEntropy.utils.helpers)

O

Orientations (class in waterEntropy.entropy.orientations)

P

PER_MOLE_TO_PER_MOLECULE (waterEntropy.entropy.vibrations.Vibrations attribute) populate_dicts() (waterEntropy.entropy.convariances.CovarianceCollection method) (waterEntropy.entropy.vibrations.Vibrations method)

print_frame_solvent_dicts() (in module waterEntropy.recipes.interfacial_solvent) print_frame_solvent_shells() (in module waterEntropy.recipes.interfacial_solvent) print_Sorient_dicts() (in module waterEntropy.entropy.orientations) print_Svib_data() (in module waterEntropy.entropy.vibrations)

S

save_solvent_indices() (in module waterEntropy.recipes.interfacial_solvent) save_solvent_shells() (in module waterEntropy.recipes.interfacial_solvent) set_property() (waterEntropy.analysis.shells.ShellCollection method) Shell (class in waterEntropy.analysis.shells) ShellCollection (class in waterEntropy.analysis.shells)

slurm_configure_cluster() (in module waterEntropy.utils.dask_clusters) slurm_directives() (in module waterEntropy.utils.dask_clusters) slurm_prologues() (in module waterEntropy.utils.dask_clusters) slurm_submit_master() (in module waterEntropy.utils.dask_clusters) system_network_interface() (in module waterEntropy.utils.dask_clusters)

U

update_counts() (waterEntropy.entropy.convariances.CovarianceCollection method)

V

Vibrations (class in waterEntropy.entropy.vibrations)

W

waterEntropy module waterEntropy.analysis module waterEntropy.analysis.HB module waterEntropy.analysis.HB_labels module waterEntropy.analysis.RAD module waterEntropy.analysis.shell_labels module waterEntropy.analysis.shells module waterEntropy.entropy module waterEntropy.entropy.convariances module waterEntropy.entropy.orientations module waterEntropy.entropy.vibrations module

waterEntropy.maths module waterEntropy.maths.transformations module waterEntropy.maths.trig module waterEntropy.recipes module waterEntropy.recipes.bulk_water module waterEntropy.recipes.forces_torques module waterEntropy.recipes.interfacial_solvent module waterEntropy.utils module waterEntropy.utils.dask_clusters module waterEntropy.utils.helpers module waterEntropy.utils.selections module WaterOrientCalculator (class in waterEntropy.entropy.orientations)