Index

A

A() (kbkit.kbi.thermodynamics.KBThermo method) activity_metadata (kbkit.kbi.thermodynamics.KBThermo property) ActivityCoefficientResult (class in kbkit.schema.activity_metadata) ActivityMetadata (class in kbkit.schema.activity_metadata) add_kbi() (kbkit.kbi.integrator.KBIntegrator method)

add_kbi_value() (kbkit.kbi.integrator.KBIntegrator method) add_lkbi() (kbkit.kbi.integrator.KBIntegrator method) add_lkbi_fit() (kbkit.kbi.integrator.KBIntegrator method) atom_counts (kbkit.io.gro.GroParser property) available_properties() (kbkit.io.edr.EdrParser method)

B

B() (kbkit.kbi.thermodynamics.KBThermo method) box_volume (kbkit.io.gro.GroParser property) (kbkit.io.top.TopParser property)

by_types (kbkit.schema.activity_metadata.ActivityMetadata property)

C

calculator (kbkit.api.pipeline.Pipeline property) compute_geometric_extrapolation() (kbkit.kbi.integrator.KBIntegrator method) compute_hr() (kbkit.kbi.integrator.KBIntegrator method) compute_kbi() (kbkit.kbi.integrator.KBIntegrator method)

compute_running_kbi() (kbkit.kbi.integrator.KBIntegrator method) configurational_enthalpy() (kbkit.io.edr.EdrParser method) cp() (kbkit.io.edr.EdrParser method) cv() (kbkit.io.edr.EdrParser method)

D

data (kbkit.io.edr.EdrParser property) DEFAULT_UNITS (kbkit.io.edr.EdrParser attribute) delta_ij (kbkit.kbi.thermodynamics.KBThermo property)

det_H() (kbkit.kbi.thermodynamics.KBThermo method) dlngamma_dxi() (kbkit.kbi.thermodynamics.KBThermo method) dmu_dxi() (kbkit.kbi.thermodynamics.KBThermo method)

E

EdrParser (class in kbkit.io.edr) electrolyte_basis (kbkit.systems.collection.SystemCollection property) electrolyte_kbi() (kbkit.kbi.calculator.KBICalculator method) electrolyte_molecules (kbkit.systems.collection.SystemCollection property) electrolyte_x (kbkit.systems.collection.SystemCollection property)

electron_count (kbkit.io.gro.GroParser property) (kbkit.io.top.TopParser property) energy (kbkit.systems.properties.SystemProperties property) excess_property() (kbkit.systems.collection.SystemCollection method) extract_molecules() (kbkit.io.rdf.RdfParser static method)

F

find_files() (kbkit.systems.properties.SystemProperties static method) FLUCT_PROPS (kbkit.io.edr.EdrParser attribute)

fn (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute) from_collection() (kbkit.visualization.timeseries.TimeseriesPlotter class method) from_rdf() (kbkit.kbi.integrator.KBIntegrator class method)

G

g_ex() (kbkit.kbi.thermodynamics.KBThermo method) g_id() (kbkit.kbi.thermodynamics.KBThermo method) g_mix() (kbkit.kbi.thermodynamics.KBThermo method) Gamma() (kbkit.kbi.thermodynamics.KBThermo method) geometric_extrapolation_result (kbkit.kbi.integrator.KBIntegrator property) geometric_weight() (kbkit.kbi.integrator.KBIntegrator method) get() (kbkit.io.edr.EdrParser method) (kbkit.schema.activity_metadata.ActivityMetadata method) (kbkit.systems.collection.SystemCollection method) (kbkit.systems.properties.SystemProperties method)

get_atomic_number() (kbkit.io.gro.GroParser static method) get_gmx_property() (kbkit.io.edr.EdrParser method) get_mol_index() (kbkit.systems.collection.SystemCollection method) get_units() (kbkit.systems.collection.SystemCollection method) gr_vdv (kbkit.kbi.integrator.KBIntegrator property) GROMACS_UNITS (kbkit.io.edr.EdrParser attribute) GroParser (class in kbkit.io.gro)

H

H() (kbkit.kbi.thermodynamics.KBThermo method) h_mix() (kbkit.kbi.thermodynamics.KBThermo method) has_all_required_pures() (kbkit.systems.collection.SystemCollection method)

has_fn (kbkit.schema.activity_metadata.ActivityCoefficientResult property) has_rdf() (kbkit.schema.system_metadata.SystemMetadata method) hr (kbkit.kbi.integrator.KBIntegrator property)

I

i0() (kbkit.kbi.thermodynamics.KBThermo method) i0_kappa() (kbkit.kbi.thermodynamics.KBThermo method) i0_p() (kbkit.kbi.thermodynamics.KBThermo method) i0_x() (kbkit.kbi.thermodynamics.KBThermo method) i0_xp() (kbkit.kbi.thermodynamics.KBThermo method)

ideal_property() (kbkit.systems.collection.SystemCollection method) is_pure() (kbkit.schema.system_metadata.SystemMetadata method) is_valid_element() (kbkit.io.gro.GroParser static method) isothermal_compressibility() (kbkit.io.edr.EdrParser method) (kbkit.kbi.thermodynamics.KBThermo method)

K

kbi (kbkit.kbi.integrator.KBIntegrator property) kbi() (kbkit.kbi.calculator.KBICalculator method) (kbkit.kbi.thermodynamics.KBThermo method) kbi_plotter (kbkit.api.pipeline.Pipeline property) kbi_plotter() (kbkit.kbi.calculator.KBICalculator method) kbi_res (kbkit.api.pipeline.Pipeline property) KBIAnalysisPlotter (class in kbkit.visualization.kbi) KBICalculator (class in kbkit.kbi.calculator) KBIntegrator (class in kbkit.kbi.integrator) kbkit.api.pipeline module kbkit.io.edr module kbkit.io.gro module kbkit.io.rdf module kbkit.io.top module kbkit.kbi.calculator module

kbkit.kbi.integrator module kbkit.kbi.thermodynamics module kbkit.schema.activity_metadata module kbkit.schema.property_result module kbkit.schema.system_metadata module kbkit.systems.collection module kbkit.systems.properties module kbkit.visualization.kbi module kbkit.visualization.thermo module kbkit.visualization.timeseries module KBThermo (class in kbkit.kbi.thermodynamics) kind (kbkit.schema.system_metadata.SystemMetadata attribute)

L

lngamma() (kbkit.kbi.thermodynamics.KBThermo method)

load() (kbkit.systems.collection.SystemCollection class method)

M

M() (kbkit.kbi.thermodynamics.KBThermo method) make_figures() (kbkit.api.pipeline.Pipeline method) (kbkit.visualization.thermo.ThermoPlotter method) MAX_SYMBOL_LENGTH (kbkit.io.gro.GroParser attribute) metadata (kbkit.schema.property_result.PropertyResult attribute) mixtures (kbkit.systems.collection.SystemCollection property) module kbkit.api.pipeline kbkit.io.edr kbkit.io.gro kbkit.io.rdf kbkit.io.top kbkit.kbi.calculator kbkit.kbi.integrator kbkit.kbi.thermodynamics kbkit.schema.activity_metadata kbkit.schema.property_result kbkit.schema.system_metadata kbkit.systems.collection kbkit.systems.properties kbkit.visualization.kbi kbkit.visualization.thermo kbkit.visualization.timeseries

mol (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute) molar_enthalpy() (kbkit.io.edr.EdrParser method) molar_volume() (kbkit.io.edr.EdrParser method) (kbkit.kbi.thermodynamics.KBThermo method) molecule_count (kbkit.io.gro.GroParser property) (kbkit.io.top.TopParser property) molecules (kbkit.io.gro.GroParser property) (kbkit.io.top.TopParser property) (kbkit.systems.collection.SystemCollection property)

N

n_i (kbkit.systems.collection.SystemCollection property) n_sys (kbkit.systems.collection.SystemCollection property)

name (kbkit.schema.property_result.PropertyResult attribute) (kbkit.schema.system_metadata.SystemMetadata attribute) nu (kbkit.systems.collection.SystemCollection property)

P

parse() (kbkit.io.top.TopParser method) path (kbkit.schema.system_metadata.SystemMetadata attribute) Pipeline (class in kbkit.api.pipeline) plot() (kbkit.visualization.thermo.ThermoPlotter method) (kbkit.visualization.timeseries.TimeseriesPlotter method) plot_activity_coef_deriv_fits() (kbkit.visualization.thermo.ThermoPlotter method) plot_binary_mixing() (kbkit.visualization.thermo.ThermoPlotter method) plot_composition() (kbkit.visualization.kbi.KBIAnalysisPlotter method) plot_kbi() (kbkit.kbi.integrator.KBIntegrator method) plot_kbi_compare() (kbkit.kbi.integrator.KBIntegrator method) plot_kbi_compare_extrapolation() (kbkit.kbi.integrator.KBIntegrator method) plot_kbi_extrapolation() (kbkit.kbi.integrator.KBIntegrator method)

plot_property() (kbkit.visualization.thermo.ThermoPlotter method) plot_property_ternary() (kbkit.visualization.thermo.ThermoPlotter method) plot_rkbis() (kbkit.visualization.kbi.KBIAnalysisPlotter method) plot_ternary() (kbkit.visualization.thermo.ThermoPlotter method) plotRDF() (kbkit.io.rdf.RdfParser method) plotter() (kbkit.kbi.thermodynamics.KBThermo method) property_type (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute) (kbkit.schema.property_result.PropertyResult attribute) PropertyResult (class in kbkit.schema.property_result) props (kbkit.schema.system_metadata.SystemMetadata attribute) pure_property() (kbkit.systems.collection.SystemCollection method) pures (kbkit.systems.collection.SystemCollection property)

R

R() (kbkit.kbi.thermodynamics.KBThermo method) rdf_path (kbkit.schema.system_metadata.SystemMetadata attribute) RdfParser (class in kbkit.io.rdf) report_skipped() (kbkit.io.top.TopParser method) residue_counts (kbkit.systems.collection.SystemCollection property) residue_kbi() (kbkit.kbi.calculator.KBICalculator method) residue_molecules (kbkit.systems.collection.SystemCollection property) residue_x (kbkit.systems.collection.SystemCollection property)

residues (kbkit.io.gro.GroParser property) results (kbkit.api.pipeline.Pipeline property) (kbkit.kbi.thermodynamics.KBThermo property) (kbkit.schema.activity_metadata.ActivityMetadata attribute) (kbkit.systems.collection.SystemCollection property) rho() (kbkit.kbi.thermodynamics.KBThermo method) rkbi (kbkit.kbi.integrator.KBIntegrator property) RT() (kbkit.kbi.thermodynamics.KBThermo method) running_kbi_map (kbkit.kbi.integrator.KBIntegrator property)

S

s0_e() (kbkit.kbi.thermodynamics.KBThermo method) s0_ij() (kbkit.kbi.thermodynamics.KBThermo method) s0_kappa() (kbkit.kbi.thermodynamics.KBThermo method) s0_kappa_e() (kbkit.kbi.thermodynamics.KBThermo method) s0_p() (kbkit.kbi.thermodynamics.KBThermo method) s0_p_e() (kbkit.kbi.thermodynamics.KBThermo method) s0_x() (kbkit.kbi.thermodynamics.KBThermo method) s0_x_e() (kbkit.kbi.thermodynamics.KBThermo method)

s0_xp() (kbkit.kbi.thermodynamics.KBThermo method) s0_xp_e() (kbkit.kbi.thermodynamics.KBThermo method) s_ex() (kbkit.kbi.thermodynamics.KBThermo method) s_mix() (kbkit.kbi.thermodynamics.KBThermo method) simulated_property() (kbkit.systems.collection.SystemCollection method) SystemCollection (class in kbkit.systems.collection) SystemMetadata (class in kbkit.schema.system_metadata) SystemProperties (class in kbkit.systems.properties) systems (kbkit.api.pipeline.Pipeline property)

T

temperature() (kbkit.kbi.thermodynamics.KBThermo method) thermo (kbkit.api.pipeline.Pipeline property) thermo_plotter (kbkit.api.pipeline.Pipeline property) ThermoPlotter (class in kbkit.visualization.thermo) timeseries_plotter() (kbkit.api.pipeline.Pipeline method) (kbkit.systems.collection.SystemCollection method) (kbkit.systems.properties.SystemProperties method)

TimeseriesPlotter (class in kbkit.visualization.timeseries) to() (kbkit.schema.property_result.PropertyResult method) topology (kbkit.systems.properties.SystemProperties property) topology_properties (kbkit.systems.properties.SystemProperties property) TopParser (class in kbkit.io.top) total_molecules (kbkit.io.gro.GroParser property) (kbkit.io.top.TopParser property)

U

u0_weight() (kbkit.kbi.integrator.KBIntegrator method) u1_weight() (kbkit.kbi.integrator.KBIntegrator method) u2_weight() (kbkit.kbi.integrator.KBIntegrator method)

units (kbkit.io.edr.EdrParser property) (kbkit.schema.property_result.PropertyResult attribute) (kbkit.systems.collection.SystemCollection property)

V

v_bar() (kbkit.kbi.thermodynamics.KBThermo method)

value (kbkit.schema.property_result.PropertyResult attribute)

X

x (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute) (kbkit.systems.collection.SystemCollection property)

x_eval (kbkit.schema.activity_metadata.ActivityCoefficientResult property)

Y

y (kbkit.schema.activity_metadata.ActivityCoefficientResult attribute)

y_eval (kbkit.schema.activity_metadata.ActivityCoefficientResult property)

Z

z_bar (kbkit.kbi.thermodynamics.KBThermo property)

z_i (kbkit.kbi.thermodynamics.KBThermo property) z_i_diff (kbkit.kbi.thermodynamics.KBThermo property)