Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | W | X | Z A add_alignment() (pyhdx.models.HDXMeasurementSet method) apply_interval() (pyhdx.models.Coverage method) (pyhdx.models.CoverageSet method) array_intersection() (in module pyhdx.models) autowrap() (in module pyhdx.support) avg_peptide_length (pyhdx.models.Coverage property) B block_length (pyhdx.models.Coverage property) C calc_rfu() (pyhdx.models.HDXTimepoint method) check_bounds() (in module pyhdx.fitting) chi_squared (pyhdx.fitting.EmptyResult attribute) clean_types() (in module pyhdx.support) colors_to_pymol() (in module pyhdx.support) ColorTransformControl (class in pyhdx.web.controllers) contiguous_regions() (in module pyhdx.models) Coverage (class in pyhdx.models) coverage (pyhdx.models.HDXMeasurement attribute) CoverageSet (class in pyhdx.models) csv_to_dataframe() (in module pyhdx.fileIO) csv_to_hdxm() (in module pyhdx.fileIO) csv_to_protein() (in module pyhdx.fileIO) D d_exp (pyhdx.models.HDXMeasurement property) (pyhdx.models.HDXMeasurementSet attribute) (pyhdx.models.HDXTimepoint property) d_uptake_cost_func() (in module pyhdx.fitting) data (pyhdx.models.HDXMeasurement attribute) dataframe_to_file() (in module pyhdx.fileIO) dataframe_to_stringio() (in module pyhdx.fileIO) DeltaGFit (class in pyhdx.fitting_torch) dG (pyhdx.fitting_torch.TorchFitResult property) DifferentialControl (class in pyhdx.web.controllers) DUptakeFitResult (class in pyhdx.fitting) DUptakeFitResultSet (class in pyhdx.fitting) E EmptyResult (class in pyhdx.fitting) estimate_errors() (in module pyhdx.fitting_torch) eval() (pyhdx.fitting_torch.TorchFitResult method) exchanges (pyhdx.models.HDXMeasurementSet property) exposure (pyhdx.models.HDXTimepoint attribute) exposures (pyhdx.models.PeptideMasterTable property) F FigureExportControl (class in pyhdx.web.controllers) FileExportControl (class in pyhdx.web.controllers) fit_d_uptake() (in module pyhdx.fitting) fit_gibbs_global() (in module pyhdx.fitting) fit_gibbs_global_batch() (in module pyhdx.fitting) fit_gibbs_global_batch_aligned() (in module pyhdx.fitting) fit_kinetics() (in module pyhdx.fitting) fit_rates() (in module pyhdx.fitting) fit_rates_half_time_interpolate() (in module pyhdx.fitting) fit_rates_weighted_average() (in module pyhdx.fitting) FitControl (class in pyhdx.web.controllers) FitReport (class in pyhdx.output) forward() (pyhdx.fitting_torch.DeltaGFit method) G gen_subclasses() (in module pyhdx.support) generate_output() (pyhdx.fitting_torch.TorchFitResult static method) GenericFitResult (class in pyhdx.fitting) get() (pyhdx.models.HDXMeasurementSet method) get_bounds() (in module pyhdx.fitting) get_d() (pyhdx.fitting.KineticsFitResult method) get_data() (pyhdx.models.PeptideMasterTable method) get_dcalc() (pyhdx.fitting_torch.TorchFitResult method) get_k_int() (pyhdx.models.Protein method) get_masks() (pyhdx.models.CoverageSet method) get_p() (pyhdx.fitting.KineticsFitResult method) get_param() (pyhdx.fitting.KineticsFitResult method) get_peptide_mse() (pyhdx.fitting_torch.TorchFitResult method) get_residue_mse() (pyhdx.fitting_torch.TorchFitResult method) get_sections() (pyhdx.models.Coverage method) get_squared_errors() (pyhdx.fitting_torch.TorchFitResult method) get_state() (pyhdx.models.PeptideMasterTable method) get_tensors() (pyhdx.models.HDXMeasurement method) (pyhdx.models.HDXMeasurementSet method) GraphControl (class in pyhdx.web.controllers) grouper() (in module pyhdx.support) guess_deltaG() (pyhdx.models.HDXMeasurement method) (pyhdx.models.HDXMeasurementSet method) H hdx_intersection() (in module pyhdx.models) HDXMeasurement (class in pyhdx.models) HDXMeasurementSet (class in pyhdx.models) HDXTimepoint (class in pyhdx.models) hex_to_rgb() (in module pyhdx.support) I index (pyhdx.models.Coverage property) (pyhdx.models.CoverageSet property) InitialGuessControl (class in pyhdx.web.controllers) K KineticsFitResult (class in pyhdx.fitting) L load_fitresult() (in module pyhdx.fileIO) LocalThreadExecutor (class in pyhdx.output) M make_color_array() (in module pyhdx.support) make_monomer() (in module pyhdx.support) module pyhdx.fileIO pyhdx.fitting pyhdx.fitting_torch pyhdx.models pyhdx.output pyhdx.support mse_loss (pyhdx.fitting_torch.TorchFitResult property) multi_otsu() (in module pyhdx.support) N name (pyhdx.models.HDXMeasurement property) (pyhdx.models.HDXTimepoint property) Np (pyhdx.models.Coverage property) (pyhdx.models.HDXMeasurement property) Nr (pyhdx.models.Coverage property) (pyhdx.models.HDXMeasurement property) Nt (pyhdx.models.HDXMeasurement property) O output (pyhdx.fitting.KineticsFitResult property) P params (pyhdx.fitting.EmptyResult attribute) pbar_decorator() (in module pyhdx.support) PeptideFileInputControl (class in pyhdx.web.controllers) PeptideMasterTable (class in pyhdx.models) peptides (pyhdx.models.HDXMeasurement attribute) percent_coverage (pyhdx.models.Coverage property) pH (pyhdx.models.HDXMeasurement property) pprint_df_to_file() (in module pyhdx.support) propagate_errors() (pyhdx.models.HDXTimepoint method) Protein (class in pyhdx.models) ProteinControl (class in pyhdx.web.controllers) pyhdx.fileIO module pyhdx.fitting module pyhdx.fitting_torch module pyhdx.models module pyhdx.output module pyhdx.support module R r_number (pyhdx.models.Coverage property) rate (pyhdx.fitting.KineticsFitResult property) RatesFitResult (class in pyhdx.fitting) read_dynamx() (in module pyhdx.fileIO) reduce_inter() (in module pyhdx.support) redundancy (pyhdx.models.Coverage property) reg_loss (pyhdx.fitting_torch.TorchFitResult property) regularization_percentage (pyhdx.fitting_torch.TorchFitResult property) result (pyhdx.fitting.DUptakeFitResult attribute) rfu_peptides (pyhdx.models.HDXMeasurement property) (pyhdx.models.HDXTimepoint property) rfu_residues (pyhdx.models.HDXMeasurement property) (pyhdx.models.HDXMeasurementSet property) (pyhdx.models.HDXTimepoint property) rfu_residues_sd (pyhdx.models.HDXMeasurement property) (pyhdx.models.HDXTimepoint property) rgb_to_hex() (in module pyhdx.support) run_optimizer() (in module pyhdx.fitting) S s_r_mask (pyhdx.models.CoverageSet property) save_fitresult() (in module pyhdx.fileIO) scale() (in module pyhdx.support) select() (pyhdx.models.PeptideMasterTable method) select_config() (in module pyhdx.support) series_to_pymol() (in module pyhdx.support) SessionManagerControl (class in pyhdx.web.controllers) set_backexchange() (pyhdx.models.PeptideMasterTable method) set_control() (pyhdx.models.PeptideMasterTable method) shutdown() (pyhdx.output.LocalThreadExecutor method) state (pyhdx.models.HDXMeasurement attribute) (pyhdx.models.HDXTimepoint attribute) states (pyhdx.models.PeptideMasterTable property) submit() (pyhdx.output.LocalThreadExecutor method) T tau (pyhdx.fitting.KineticsFitResult property) temperature (pyhdx.models.HDXMeasurement property) timepoints (pyhdx.models.HDXMeasurement attribute) (pyhdx.models.HDXMeasurementSet attribute) to_file() (pyhdx.fitting_torch.TorchFitResult method) (pyhdx.fitting_torch.TorchFitResultSet method) (pyhdx.models.HDXMeasurement method) (pyhdx.models.HDXMeasurementSet method) (pyhdx.models.Protein method) TorchFitResult (class in pyhdx.fitting_torch) TorchFitResultSet (class in pyhdx.fitting_torch) total_loss (pyhdx.fitting_torch.TorchFitResult property) try_wrap() (in module pyhdx.support) W weighted_average() (pyhdx.models.HDXTimepoint method) X X (pyhdx.models.Coverage attribute) X_norm (pyhdx.models.Coverage property) Z Z (pyhdx.models.Coverage attribute) Z_norm (pyhdx.models.Coverage property)