Index

_

__init__() (pykingenie.fitter.KineticsFitterGeneral method) (pykingenie.fitter_solution.KineticsFitterSolution method) (pykingenie.fitter_surface.KineticsFitter method) (pykingenie.gator.GatorExperiment method) (pykingenie.kingenie_solution.KinGenieCsvSolution method) (pykingenie.kingenie_surface.KinGenieCsv method) (pykingenie.main.KineticsAnalyzer method) (pykingenie.octet.OctetExperiment method) (pykingenie.solution_exp.SolutionBasedExp method) (pykingenie.surface_exp.SurfaceBasedExperiment method)

A

add_experiment() (pykingenie.main.KineticsAnalyzer method) add_fitting() (pykingenie.main.KineticsAnalyzer method) align_association() (pykingenie.surface_exp.SurfaceBasedExperiment method)

align_dissociation() (pykingenie.surface_exp.SurfaceBasedExperiment method) assoc_lst (pykingenie.fitter_solution.KineticsFitterSolution attribute) (pykingenie.fitter_surface.KineticsFitter attribute) average() (pykingenie.surface_exp.SurfaceBasedExperiment method)

C

calculate_asymmetric_error() (pykingenie.main.KineticsAnalyzer method) calculate_ci95() (pykingenie.fitter_surface.KineticsFitter method) check_sensor_name() (pykingenie.surface_exp.SurfaceBasedExperiment method) clear_fittings() (pykingenie.fitter.KineticsFitterGeneral method) combine_dicts() (in module pykingenie.utils.processing) combine_sequences() (in module pykingenie.utils.processing) conc_df (pykingenie.kingenie_solution.KinGenieCsvSolution attribute) (pykingenie.solution_exp.SolutionBasedExp attribute)

concat_signal_lst() (in module pykingenie.utils.processing) config_fig() (in module pykingenie.utils.plotting) constant_vector_conformational_selection() (in module pykingenie.utils.signal_surface) constant_vector_induced_fit() (in module pykingenie.utils.signal_surface) convert_to_numbers() (pykingenie.octet.OctetExperiment method) create_fitting_bounds_table() (pykingenie.fitter.KineticsFitterGeneral method) create_unique_sensor_names() (pykingenie.surface_exp.SurfaceBasedExperiment method) create_unique_traces_names() (pykingenie.solution_exp.SolutionBasedExp method) cut_off_time() (pykingenie.solution_exp.SolutionBasedExp method)

D

delete_experiment() (pykingenie.main.KineticsAnalyzer method) detect_time_list_continuos() (in module pykingenie.utils.processing) df_steps (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute) differential_matrix_association_conformational_selection() (in module pykingenie.utils.signal_surface)

differential_matrix_association_induced_fit() (in module pykingenie.utils.signal_surface) differential_matrix_dissociation_conformational_selection() (in module pykingenie.utils.signal_surface) differential_matrix_dissociation_induced_fit() (in module pykingenie.utils.signal_surface) discard_steps() (pykingenie.surface_exp.SurfaceBasedExperiment method) disso_lst (pykingenie.fitter_surface.KineticsFitter attribute) double_exponential() (in module pykingenie.utils.math)

E

etree_to_dict() (in module pykingenie.utils.processing) exp_info (pykingenie.octet.OctetExperiment attribute)

expand_parameter_list() (in module pykingenie.utils.processing) experiment_names (pykingenie.main.KineticsAnalyzer attribute) experiments (pykingenie.main.KineticsAnalyzer attribute)

F

find_index_of_previous_step_type() (in module pykingenie.utils.processing) find_initial_parameters_induced_fit_solution() (in module pykingenie.utils.fitting_solution) find_initial_params_if() (pykingenie.fitter_solution.KineticsFitterSolution method) find_loading_column() (in module pykingenie.utils.processing) fit_double_exponential() (in module pykingenie.utils.fitting_general) fit_double_exponentials() (pykingenie.fitter_solution.KineticsFitterSolution method) fit_induced_fit() (pykingenie.fitter_solution.KineticsFitterSolution method) fit_induced_fit_sites_assoc_and_disso() (in module pykingenie.utils.fitting_surface) fit_induced_fit_solution() (in module pykingenie.utils.fitting_solution) fit_one_binding_site() (pykingenie.fitter_solution.KineticsFitterSolution method) fit_one_site_assoc_and_disso() (in module pykingenie.utils.fitting_surface) (pykingenie.fitter_surface.KineticsFitter method) fit_one_site_assoc_and_disso_ktr() (in module pykingenie.utils.fitting_surface) fit_one_site_association() (in module pykingenie.utils.fitting_surface) (pykingenie.fitter_surface.KineticsFitter method) fit_one_site_dissociation() (in module pykingenie.utils.fitting_surface) (pykingenie.fitter_surface.KineticsFitter method)

fit_one_site_if_assoc_and_disso() (pykingenie.fitter_surface.KineticsFitter method) fit_one_site_solution() (in module pykingenie.utils.fitting_solution) fit_params_kinetics (pykingenie.fitter.KineticsFitterGeneral attribute) (pykingenie.fitter_solution.KineticsFitterSolution attribute) (pykingenie.fitter_surface.KineticsFitter attribute) fit_params_ss (pykingenie.fitter.KineticsFitterGeneral attribute) (pykingenie.fitter_solution.KineticsFitterSolution attribute) (pykingenie.fitter_surface.KineticsFitter attribute) fit_single_exponential() (in module pykingenie.utils.fitting_general) fit_single_exponentials() (pykingenie.fitter_solution.KineticsFitterSolution method) (pykingenie.fitter_surface.KineticsFitter method) fit_steady_state() (pykingenie.fitter_surface.KineticsFitter method) fit_steady_state_one_site() (in module pykingenie.utils.fitting_surface) fitted_params_boundaries (pykingenie.fitter.KineticsFitterGeneral attribute) fittings (pykingenie.main.KineticsAnalyzer attribute) fittings_names (pykingenie.main.KineticsAnalyzer attribute) fn (pykingenie.kingenie_surface.KinGenieCsv attribute) fns (pykingenie.octet.OctetExperiment attribute)

G

GatorExperiment (class in pykingenie.gator) generate_fittings() (pykingenie.main.KineticsAnalyzer method) generate_fittings_solution() (pykingenie.main.KineticsAnalyzer method) generate_ligand_conc_df() (pykingenie.octet.OctetExperiment method) get_colors_from_numeric_values() (in module pykingenie.utils.processing) get_desired_rss() (in module pykingenie.utils.math) get_experiment_properties() (pykingenie.main.KineticsAnalyzer method) get_fitting_results() (pykingenie.main.KineticsAnalyzer method) get_initial_concentration_conformational_selection() (in module pykingenie.utils.signal_solution) get_k_off_initial_guess() (pykingenie.fitter_surface.KineticsFitter method) get_kobs_conformational_selection() (in module pykingenie.utils.signal_solution) get_kobs_induced_fit() (in module pykingenie.utils.signal_solution) get_legends_table() (pykingenie.main.KineticsAnalyzer method)

get_palette() (in module pykingenie.utils.processing) get_plotting_df() (in module pykingenie.utils.processing) get_rss() (in module pykingenie.utils.math) get_smax_upper_bound_factor() (in module pykingenie.utils.fitting_surface) get_steady_state() (pykingenie.fitter_solution.KineticsFitterSolution method) (pykingenie.fitter_surface.KineticsFitter method) get_step_xy() (pykingenie.surface_exp.SurfaceBasedExperiment method) get_trace_xy() (pykingenie.solution_exp.SolutionBasedExp method) group_double_exponential_k_obs_by_protein_concentration() (pykingenie.fitter_solution.KineticsFitterSolution method) group_k_obs_by_protein_concentration() (pykingenie.fitter_solution.KineticsFitterSolution method) guess_experiment_name() (in module pykingenie.utils.processing) guess_experiment_type() (in module pykingenie.utils.processing) guess_initial_signal() (in module pykingenie.utils.fitting_surface)

H

head (pykingenie.octet.OctetExperiment.ligand_conc_df attribute) (pykingenie.octet.OctetExperiment.steps_performed attribute)

high_bounds (pykingenie.fitter.KineticsFitterGeneral attribute)

I

if_string_to_list() (in module pykingenie.utils.processing)

init_fittings() (pykingenie.main.KineticsAnalyzer method) is_single_cycle (pykingenie.fitter_surface.KineticsFitter attribute)

K

KineticsAnalyzer (class in pykingenie.main) KineticsFitter (class in pykingenie.fitter_surface) KineticsFitterGeneral (class in pykingenie.fitter)

KineticsFitterSolution (class in pykingenie.fitter_solution) KinGenieCsv (class in pykingenie.kingenie_surface) KinGenieCsvSolution (class in pykingenie.kingenie_solution)

L

lig_conc (pykingenie.fitter_solution.KineticsFitterSolution attribute) lig_conc_lst (pykingenie.fitter_surface.KineticsFitter attribute) lig_conc_lst_per_id (pykingenie.fitter_surface.KineticsFitter attribute)

ligand_conc_df (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute) low_bounds (pykingenie.fitter.KineticsFitterGeneral attribute)

M

median_filter() (in module pykingenie.utils.math) merge_conc_df_solution() (pykingenie.main.KineticsAnalyzer method) merge_consecutive_steps() (pykingenie.octet.OctetExperiment method) merge_consecutive_steps_by_name() (pykingenie.octet.OctetExperiment method) merge_ligand_conc_df() (pykingenie.main.KineticsAnalyzer method) module pykingenie pykingenie.fitter pykingenie.fitter_solution pykingenie.fitter_surface pykingenie.gator pykingenie.kingenie_solution pykingenie.kingenie_surface pykingenie.main pykingenie.octet pykingenie.solution_exp pykingenie.surface_exp pykingenie.utils pykingenie.utils.fitting_general pykingenie.utils.fitting_solution pykingenie.utils.fitting_surface pykingenie.utils.math pykingenie.utils.palettes pykingenie.utils.plotting pykingenie.utils.processing pykingenie.utils.signal_solution pykingenie.utils.signal_surface

N

name (pykingenie.fitter_solution.KineticsFitterSolution attribute) (pykingenie.kingenie_solution.KinGenieCsvSolution attribute) (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) (pykingenie.solution_exp.SolutionBasedExp attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute)

names (pykingenie.fitter_surface.KineticsFitter attribute) no_sensors (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) no_steps (pykingenie.octet.OctetExperiment attribute) no_traces (pykingenie.kingenie_solution.KinGenieCsvSolution attribute) (pykingenie.solution_exp.SolutionBasedExp attribute)

O

OctetExperiment (class in pykingenie.octet) ode_conformational_selection_insolution() (in module pykingenie.utils.signal_solution) ode_induced_fit_insolution() (in module pykingenie.utils.signal_solution) ode_mixture_analyte_association() (in module pykingenie.utils.signal_surface) ode_mixture_analyte_dissociation() (in module pykingenie.utils.signal_surface) ode_one_site_insolution() (in module pykingenie.utils.signal_solution)

ode_one_site_mass_transport_association() (in module pykingenie.utils.signal_surface) ode_one_site_mass_transport_dissociation() (in module pykingenie.utils.signal_surface) one_site_assoc_and_disso_asymmetric_ci95() (in module pykingenie.utils.fitting_surface) one_site_assoc_and_disso_asymmetric_ci95_koff() (in module pykingenie.utils.fitting_surface) one_site_association_analytical() (in module pykingenie.utils.signal_surface) one_site_dissociation_analytical() (in module pykingenie.utils.signal_surface)

P

params (pykingenie.fitter.KineticsFitterGeneral attribute) plot_association_dissociation() (in module pykingenie.utils.plotting) plot_plate_info() (in module pykingenie.utils.plotting) plot_steady_state() (in module pykingenie.utils.plotting) plot_traces() (in module pykingenie.utils.plotting) plot_traces_all() (in module pykingenie.utils.plotting) prot_conc (pykingenie.fitter_solution.KineticsFitterSolution attribute) pykingenie module pykingenie.fitter module pykingenie.fitter_solution module pykingenie.fitter_surface module pykingenie.gator module pykingenie.kingenie_solution module pykingenie.kingenie_surface module pykingenie.main module pykingenie.octet module

pykingenie.solution_exp module pykingenie.surface_exp module pykingenie.utils module pykingenie.utils.fitting_general module pykingenie.utils.fitting_solution module pykingenie.utils.fitting_surface module pykingenie.utils.math module pykingenie.utils.palettes module pykingenie.utils.plotting module pykingenie.utils.processing module pykingenie.utils.signal_solution module pykingenie.utils.signal_surface module

R

re_fit() (in module pykingenie.utils.fitting_general) re_fit_2() (in module pykingenie.utils.fitting_general) read_all_gator_data() (pykingenie.gator.GatorExperiment method) read_csv() (pykingenie.kingenie_solution.KinGenieCsvSolution method) (pykingenie.kingenie_surface.KinGenieCsv method)

read_experiment_ini() (pykingenie.gator.GatorExperiment method) read_sample_plate_info() (pykingenie.octet.OctetExperiment method) read_sensor_data() (pykingenie.gator.GatorExperiment method) (pykingenie.octet.OctetExperiment method) read_settings_ini() (pykingenie.gator.GatorExperiment method) rss_p() (in module pykingenie.utils.math)

S

sample_column (pykingenie.octet.OctetExperiment attribute) sample_conc (pykingenie.octet.OctetExperiment attribute) sample_conc_labeled (pykingenie.octet.OctetExperiment attribute) sample_id (pykingenie.octet.OctetExperiment attribute) sample_plate_loaded (pykingenie.octet.OctetExperiment attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute) sample_row (pykingenie.octet.OctetExperiment attribute) sample_type (pykingenie.octet.OctetExperiment attribute) sample_type_to_letter() (in module pykingenie.utils.processing) sensor_names (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute) sensor_names_unique (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) set1_colors (in module pykingenie.utils.palettes) set3_colors (in module pykingenie.utils.palettes) signal_assoc_fit (pykingenie.fitter.KineticsFitterGeneral attribute) (pykingenie.fitter_solution.KineticsFitterSolution attribute) (pykingenie.fitter_surface.KineticsFitter attribute) signal_disso_fit (pykingenie.fitter.KineticsFitterGeneral attribute) (pykingenie.fitter_surface.KineticsFitter attribute) signal_ode_conformational_selection_insolution() (in module pykingenie.utils.signal_solution) signal_ode_induced_fit_insolution() (in module pykingenie.utils.signal_solution) signal_ode_one_site_insolution() (in module pykingenie.utils.signal_solution) signal_ss (pykingenie.fitter_solution.KineticsFitterSolution attribute) (pykingenie.fitter_surface.KineticsFitter attribute) signal_ss_fit (pykingenie.fitter.KineticsFitterGeneral attribute) (pykingenie.fitter_solution.KineticsFitterSolution attribute) (pykingenie.fitter_surface.KineticsFitter attribute)

single_exponential() (in module pykingenie.utils.math) smax_guesses_shared (pykingenie.fitter_surface.KineticsFitter attribute) smax_guesses_unq (pykingenie.fitter_surface.KineticsFitter attribute) SolutionBasedExp (class in pykingenie.solution_exp) solve_all_states_fast() (in module pykingenie.utils.signal_surface) solve_conformational_selection_association() (in module pykingenie.utils.signal_surface) solve_conformational_selection_dissociation() (in module pykingenie.utils.signal_surface) solve_induced_fit_association() (in module pykingenie.utils.signal_surface) solve_induced_fit_dissociation() (in module pykingenie.utils.signal_surface) solve_ode_conformational_selection_insolution() (in module pykingenie.utils.signal_solution) solve_ode_induced_fit_insolution() (in module pykingenie.utils.signal_solution) solve_ode_mixture_analyte_association() (in module pykingenie.utils.signal_surface) solve_ode_mixture_analyte_dissociation() (in module pykingenie.utils.signal_surface) solve_ode_one_site_insolution() (in module pykingenie.utils.signal_solution) solve_ode_one_site_mass_transport_association() (in module pykingenie.utils.signal_surface) solve_ode_one_site_mass_transport_dissociation() (in module pykingenie.utils.signal_surface) solve_steady_state() (in module pykingenie.utils.signal_surface) steady_state_one_site() (in module pykingenie.utils.signal_surface) steady_state_one_site_asymmetric_ci95() (in module pykingenie.utils.fitting_surface) step_info (pykingenie.octet.OctetExperiment attribute) steps_performed (pykingenie.octet.OctetExperiment attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute) submit_fitting_solution() (pykingenie.main.KineticsAnalyzer method) submit_kinetics_fitting() (pykingenie.main.KineticsAnalyzer method) submit_steady_state_fitting() (pykingenie.main.KineticsAnalyzer method) subset_data() (in module pykingenie.utils.processing) subtraction() (pykingenie.surface_exp.SurfaceBasedExperiment method) subtraction_one_to_one() (pykingenie.surface_exp.SurfaceBasedExperiment method) SurfaceBasedExperiment (class in pykingenie.surface_exp)

T

time_assoc_lst (pykingenie.fitter_solution.KineticsFitterSolution attribute) (pykingenie.fitter_surface.KineticsFitter attribute) time_disso_lst (pykingenie.fitter_surface.KineticsFitter attribute) traces_loaded (pykingenie.kingenie_solution.KinGenieCsvSolution attribute) (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) (pykingenie.solution_exp.SolutionBasedExp attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute)

traces_names (pykingenie.kingenie_solution.KinGenieCsvSolution attribute) (pykingenie.solution_exp.SolutionBasedExp attribute) traces_names_unique (pykingenie.kingenie_solution.KinGenieCsvSolution attribute) (pykingenie.solution_exp.SolutionBasedExp attribute) type (pykingenie.solution_exp.SolutionBasedExp attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute)

V

VIRIDIS (in module pykingenie.utils.palettes)

X

xs (pykingenie.kingenie_solution.KinGenieCsvSolution attribute) (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) (pykingenie.solution_exp.SolutionBasedExp attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute)

Y

ys (pykingenie.kingenie_solution.KinGenieCsvSolution attribute) (pykingenie.kingenie_surface.KinGenieCsv attribute) (pykingenie.octet.OctetExperiment attribute) (pykingenie.solution_exp.SolutionBasedExp attribute) (pykingenie.surface_exp.SurfaceBasedExperiment attribute)