Index

_

__init__() (solvation_analysis.coordination.Coordination method) (solvation_analysis.networking.Networking method) (solvation_analysis.pairing.Pairing method) (solvation_analysis.residence.Residence method) (solvation_analysis.solute.Solute method) (solvation_analysis.speciation.Speciation method)

A

auto_covariances (solvation_analysis.residence.Residence property)

C

calculate_shell_fraction() (solvation_analysis.speciation.Speciation method) compare_coordination_numbers() (in module solvation_analysis.plotting) compare_coordination_vs_random() (in module solvation_analysis.plotting) compare_diluent() (in module solvation_analysis.plotting) compare_free_solvents() (in module solvation_analysis.plotting) compare_pairing() (in module solvation_analysis.plotting) compare_residence_times_cutoff() (in module solvation_analysis.plotting)

compare_residence_times_fit() (in module solvation_analysis.plotting) compare_solvent_dicts() (in module solvation_analysis.plotting) coordinating_atoms (solvation_analysis.coordination.Coordination property) Coordination (class in solvation_analysis.coordination) coordination_numbers (solvation_analysis.coordination.Coordination property) coordination_numbers_by_frame (solvation_analysis.coordination.Coordination property) coordination_vs_random (solvation_analysis.coordination.Coordination property)

D

diluent_composition (solvation_analysis.pairing.Pairing property) diluent_composition_by_frame (solvation_analysis.pairing.Pairing property)

diluent_counts (solvation_analysis.pairing.Pairing property) draw_molecule() (solvation_analysis.solute.Solute method)

F

fit_parameters (solvation_analysis.residence.Residence property) fraction_free_solvents (solvation_analysis.pairing.Pairing property) from_atoms() (solvation_analysis.solute.Solute static method) from_atoms_dict() (solvation_analysis.solute.Solute static method) from_solute() (solvation_analysis.coordination.Coordination static method) (solvation_analysis.networking.Networking static method) (solvation_analysis.pairing.Pairing static method) (solvation_analysis.residence.Residence static method) (solvation_analysis.speciation.Speciation static method)

from_solute_list() (solvation_analysis.solute.Solute static method)

G

get_closest_n_mol() (solvation_analysis.solute.Solute method) get_network_res_ix() (solvation_analysis.networking.Networking method)

get_shell() (solvation_analysis.solute.Solute method) get_shells() (solvation_analysis.speciation.Speciation method)

M

module solvation_analysis.coordination solvation_analysis.networking solvation_analysis.pairing solvation_analysis.plotting solvation_analysis.residence solvation_analysis.solute solvation_analysis.speciation

N

network_df (solvation_analysis.networking.Networking property)

network_sizes (solvation_analysis.networking.Networking property) Networking (class in solvation_analysis.networking)

P

Pairing (class in solvation_analysis.pairing) pairing_by_frame (solvation_analysis.pairing.Pairing property) plot_auto_covariance() (solvation_analysis.residence.Residence method) plot_co_occurrence() (in module solvation_analysis.plotting)

plot_network_size_histogram() (in module solvation_analysis.plotting) plot_rdfs() (in module solvation_analysis.plotting) plot_shell_composition_by_size() (in module solvation_analysis.plotting) plot_solvation_radius() (solvation_analysis.solute.Solute method) plot_speciation() (in module solvation_analysis.plotting)

R

radial_shell() (solvation_analysis.solute.Solute method) Residence (class in solvation_analysis.residence)

residence_times_cutoff (solvation_analysis.residence.Residence property) residence_times_fit (solvation_analysis.residence.Residence property)

S

Solute (class in solvation_analysis.solute) solute_status (solvation_analysis.networking.Networking property) solute_status_by_frame (solvation_analysis.networking.Networking property) solvation_analysis.coordination module solvation_analysis.networking module solvation_analysis.pairing module solvation_analysis.plotting module

solvation_analysis.residence module solvation_analysis.solute module solvation_analysis.speciation module solvent_co_occurrence (solvation_analysis.speciation.Speciation property) solvent_pairing (solvation_analysis.pairing.Pairing property) Speciation (class in solvation_analysis.speciation) speciation_data (solvation_analysis.speciation.Speciation property) speciation_fraction (solvation_analysis.speciation.Speciation property)