Index

A

alk_ua_APSP() (INDUSAnalysis.contacts.ContactsAnalysis method)

args (INDUSAnalysis.timeseries.TimeSeriesAnalysis attribute)

B

bootstrap_independent_sample() (in module INDUSAnalysis.timeseries) buried_surface_classifier() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_classifier)

buried_surface_ensemble_classifier() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_ensemble_classifier) buried_surface_valueslist() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars)

C

calc_deviation_worker() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) calc_deviations() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) calc_plot_histogram_contacts() (INDUSAnalysis.contacts.ContactsAnalysis method) calc_probe_waters() (INDUSAnalysis.indus_waters.WatersAnalysis method) calc_Rg() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) calc_Rg_worker() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) calc_RMSD() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) calc_RMSD_worker() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method)

calc_trajcontacts() (INDUSAnalysis.contacts.ContactsAnalysis method) calc_trajcontacts_alk_ua() (INDUSAnalysis.contacts.ContactsAnalysis method) calc_trajcontacts_atomic_h() (INDUSAnalysis.contacts.ContactsAnalysis method) calc_trajcontacts_atomic_sh() (INDUSAnalysis.contacts.ContactsAnalysis method) charged_hydrophobic_hydrophilic_residues_valueslist() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars) ContactsAnalysis (class in INDUSAnalysis.contacts) correct_contiguous (INDUSAnalysis.timeseries.TimeSeries attribute) create1DTimeSeries() (in module INDUSAnalysis.timeseries) cumulative_moving_average() (INDUSAnalysis.timeseries.TimeSeries method)

D

data (INDUSAnalysis.timeseries.TimeSeries attribute)

data_array (INDUSAnalysis.timeseries.TimeSeries property) derivative_integrated_step_gaussian() (in module INDUSAnalysis.lib.collective)

E

energy_overlap() (in module INDUSAnalysis.ensemble.polymers.umbrella_sampling_utils)

estimate_kappa() (in module INDUSAnalysis.ensemble.polymers.umbrella_sampling_utils) estimate_min_max_Nstar() (in module INDUSAnalysis.ensemble.polymers.umbrella_sampling_utils)

F

fit_integrated_step_gaussian() (in module INDUSAnalysis.lib.collective)

fit_linear_model() (in module INDUSAnalysis.lib.collective)

H

hydrated_atom_chars() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars)

I

INDUSAnalysis module INDUSAnalysis.contacts module INDUSAnalysis.ensemble module INDUSAnalysis.ensemble.polymers module INDUSAnalysis.ensemble.polymers.umbrella_sampling_utils module INDUSAnalysis.ensemble.proteins module INDUSAnalysis.ensemble.proteins.denaturation module INDUSAnalysis.ensemble.proteins.denaturation.contacts module INDUSAnalysis.ensemble.proteins.denaturation.OP module INDUSAnalysis.ensemble.proteins.denaturation.OP.phi_ensemble_Rg_RMSD module INDUSAnalysis.ensemble.proteins.denaturation.OP.RMSF module INDUSAnalysis.ensemble.proteins.denaturation.vis module INDUSAnalysis.ensemble.proteins.denaturation.waters module INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_classifier module INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_ensemble_classifier module

INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars module INDUSAnalysis.ensemble.proteins.denaturation.waters.Nt_histogram_phi module INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_ensemble module INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_i_star module INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_star module INDUSAnalysis.ensemble.proteins.denaturation.waters.vis_phi_i_star module INDUSAnalysis.ensemble.proteins.dewetting module INDUSAnalysis.indus_waters module INDUSAnalysis.lib module INDUSAnalysis.lib.collective module INDUSAnalysis.lib.path module INDUSAnalysis.lib.profiling module INDUSAnalysis.protein_order_params module INDUSAnalysis.timeseries module integrated_step_gaussian() (in module INDUSAnalysis.lib.collective)

L

labels (INDUSAnalysis.timeseries.TimeSeries attribute) (INDUSAnalysis.timeseries.TimeSeries property)

linear_model() (in module INDUSAnalysis.lib.collective) load_TimeSeries() (INDUSAnalysis.timeseries.TimeSeriesAnalysis class method) loadTimeSeriesFromDAT() (in module INDUSAnalysis.timeseries)

M

mean() (INDUSAnalysis.timeseries.TimeSeries method) module INDUSAnalysis INDUSAnalysis.contacts INDUSAnalysis.ensemble INDUSAnalysis.ensemble.polymers INDUSAnalysis.ensemble.polymers.umbrella_sampling_utils INDUSAnalysis.ensemble.proteins INDUSAnalysis.ensemble.proteins.denaturation INDUSAnalysis.ensemble.proteins.denaturation.contacts INDUSAnalysis.ensemble.proteins.denaturation.OP INDUSAnalysis.ensemble.proteins.denaturation.OP.phi_ensemble_Rg_RMSD INDUSAnalysis.ensemble.proteins.denaturation.OP.RMSF INDUSAnalysis.ensemble.proteins.denaturation.vis INDUSAnalysis.ensemble.proteins.denaturation.waters INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_classifier INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_ensemble_classifier INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars INDUSAnalysis.ensemble.proteins.denaturation.waters.Nt_histogram_phi INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_ensemble INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_i_star INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_star INDUSAnalysis.ensemble.proteins.denaturation.waters.vis_phi_i_star INDUSAnalysis.ensemble.proteins.dewetting INDUSAnalysis.indus_waters INDUSAnalysis.lib INDUSAnalysis.lib.collective INDUSAnalysis.lib.path INDUSAnalysis.lib.profiling INDUSAnalysis.protein_order_params INDUSAnalysis.timeseries

moving_average() (INDUSAnalysis.timeseries.TimeSeries method)

N

nonzero_autopct() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars)

O

OrderParamsAnalysis (class in INDUSAnalysis.protein_order_params)

P

P_to_phi() (in module INDUSAnalysis.lib.collective) parse_args() (INDUSAnalysis.timeseries.TimeSeriesAnalysis method) path_s() (in module INDUSAnalysis.lib.path) path_s_scaled() (in module INDUSAnalysis.lib.path) path_z() (in module INDUSAnalysis.lib.path) path_z_scaled() (in module INDUSAnalysis.lib.path) penalized_integrated_step_gaussian() (in module INDUSAnalysis.lib.collective) phi_ensemble() (in module INDUSAnalysis.ensemble.proteins.denaturation.OP.phi_ensemble_Rg_RMSD) (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.Nt_histogram_phi) (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_ensemble) (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_star) phi_i_star() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_i_star) phi_to_P() (in module INDUSAnalysis.lib.collective) plot() (INDUSAnalysis.timeseries.TimeSeries method) plot_2d_heatmap() (INDUSAnalysis.timeseries.TimeSeries method) plot_cma_Rg() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method)

plot_cma_RMSD() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) plot_cma_waters() (INDUSAnalysis.indus_waters.WatersAnalysis method) plot_deviations() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) plot_ma_Rg() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) plot_ma_RMSD() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) plot_ma_waters() (INDUSAnalysis.indus_waters.WatersAnalysis method) plot_mean_contactmatrix() (INDUSAnalysis.contacts.ContactsAnalysis method) plot_path_s() (in module INDUSAnalysis.lib.path) plot_path_z() (in module INDUSAnalysis.lib.path) plot_probe_waters() (INDUSAnalysis.indus_waters.WatersAnalysis method) plot_Rg() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) plot_RMSD() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) plot_total_fraction_contacts() (INDUSAnalysis.contacts.ContactsAnalysis method) plot_waters() (INDUSAnalysis.indus_waters.WatersAnalysis method) polar_nonpolar_atoms_valueslist() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars) protein_heavy_APSP() (INDUSAnalysis.contacts.ContactsAnalysis method)

R

read_args() (INDUSAnalysis.contacts.ContactsAnalysis method) (INDUSAnalysis.indus_waters.WatersAnalysis method) (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) (INDUSAnalysis.timeseries.TimeSeriesAnalysis method)

read_waters() (INDUSAnalysis.indus_waters.WatersAnalysis class method) RMSF() (in module INDUSAnalysis.ensemble.proteins.denaturation.OP.RMSF)

S

save_figure() (INDUSAnalysis.timeseries.TimeSeriesAnalysis method) save_TimeSeries() (INDUSAnalysis.timeseries.TimeSeriesAnalysis class method) sec_struct_class_valueslist() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars) sec_struct_group_valueslist() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars)

skipfunc() (in module INDUSAnalysis.lib.profiling) standard_error() (INDUSAnalysis.timeseries.TimeSeries method) statisticalInefficiency() (in module INDUSAnalysis.timeseries) std() (INDUSAnalysis.timeseries.TimeSeries method)

T

time_array (INDUSAnalysis.timeseries.TimeSeries property) timefunc() (in module INDUSAnalysis.lib.profiling) timefuncfile() (in module INDUSAnalysis.lib.profiling)

times (INDUSAnalysis.timeseries.TimeSeries attribute) TimeSeries (class in INDUSAnalysis.timeseries) TimeSeriesAnalysis (class in INDUSAnalysis.timeseries)

V

vis_phi_i_star() (in module INDUSAnalysis.ensemble.proteins.denaturation.waters.vis_phi_i_star)

W

WatersAnalysis (class in INDUSAnalysis.indus_waters)

write_deviations_pdb() (INDUSAnalysis.protein_order_params.OrderParamsAnalysis method) write_probe_waters_pdb() (INDUSAnalysis.indus_waters.WatersAnalysis method)