Index Symbols | A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y Symbols --add ppr-tecan command line option --all ppr-tecan command line option --band fit-titration-spec command line option --bg ppr-tecan command line option --bg-adj ppr-tecan command line option --bg-mth ppr-tecan command line option --boot fit-titration-glob command line option --cl ppr-tecan command line option --ctr-cols ppr-detect-bad-wells command line option --ctr-free-k ppr-tecan command line option --detect-bad ppr-tecan command line option --discard-bad-wells ppr-tecan command line option --dry-run ppr-tecan command line option --fit ppr-tecan command line option --fit-method ppr-tecan command line option --is-ph fit-titration command line option --labels note_to_csv command line option --lim ppr-tecan command line option --mask-outliers ppr-tecan command line option --mcmc ppr-tecan command line option --mcmc-samples ppr-tecan command line option --no-detect-bad ppr-tecan command line option --no-discard-bad-wells ppr-tecan command line option --no-fit ppr-tecan command line option --no-is-ph fit-titration command line option --no-mask-outliers ppr-tecan command line option --no-png ppr-tecan command line option --no-weight fit-titration-glob command line option --noise-alpha ppr-tecan command line option --noise-gain ppr-tecan command line option --nrm ppr-tecan command line option --nuts-sampler ppr-tecan command line option --out fit-titration command line option ppr command line option --outlier ppr-tecan command line option --outlier-threshold ppr-tecan command line option --output note_to_csv command line option --png ppr-tecan command line option --quiet ppr command line option --sch ppr-tecan command line option --temp note_to_csv command line option --title ppr-tecan command line option --verbose fit-titration command line option ppr command line option --version clop command line option fit-titration command line option ppr command line option --weight fit-titration-glob command line option --z-threshold ppr-detect-bad-wells command line option -b fit-titration-glob command line option fit-titration-spec command line option ppr-enspire command line option -l note_to_csv command line option -o fit-titration command line option note_to_csv command line option ppr command line option -q ppr command line option -t note_to_csv command line option ppr-tecan command line option -v fit-titration command line option ppr command line option A additions (clophfit.prtecan.titration.Titration property) all_computed() (clophfit.prtecan.titration.TitrationResults static method) allequal (clophfit.prtecan.models.LabelblocksGroup attribute) almost_equal() (clophfit.prtecan.models.Labelblock method) analyze_label_bias() (in module clophfit.fitting.residuals) analyze_spectra() (in module clophfit.fitting.core) analyze_spectra_glob() (in module clophfit.fitting.core) apply_combination() (in module clophfit.prtecan.export) apply_mask() (clophfit.fitting.data_structures.Dataset method) apply_outlier_mask() (in module clophfit.fitting.utils) apply_tecan_combination() (in module clophfit.testing.fitter_test_utils) assign_error_model() (in module clophfit.fitting.utils) B bands (clophfit.fitting.data_structures.SpectraGlobResults attribute) bg (clophfit.prtecan.titration.Buffer property) (clophfit.prtecan.titration.Titration property) bg_err (clophfit.prtecan.titration.Buffer property) (clophfit.prtecan.titration.Titration property) bg_noise (clophfit.prtecan.titration.Buffer property) (clophfit.prtecan.titration.Titration property) binding_1site() (in module clophfit.fitting.models) Buffer (class in clophfit.prtecan.titration) buffer (clophfit.prtecan.models.PlateScheme property) (clophfit.prtecan.titration.Titration attribute) BufferFit (class in clophfit.prtecan.titration) build_factorized_tecan_fit_combinations() (in module clophfit.testing.fitter_test_utils) build_fitters() (in module clophfit.testing.fitter_test_utils) build_tecan_fit_combinations() (in module clophfit.testing.fitter_test_utils) build_titrations() (clophfit.prenspire.prenspire.Note method) C calculate_bias() (in module clophfit.testing.evaluation) calculate_conc() (in module clophfit.prtecan.parsers) calculate_coverage() (in module clophfit.testing.evaluation) calculate_rmse() (in module clophfit.testing.evaluation) clean_data() (clophfit.fitting.data_structures.Dataset method) clear_all_data_results() (clophfit.prtecan.titration.Titration method) CLIError clop command line option --version clop-eq1 command line option KD1 PH PKA clophfit module clophfit.clophfit_types module clophfit.fitting module clophfit.fitting.bayes module clophfit.fitting.core module clophfit.fitting.data_structures module clophfit.fitting.diagnostics module clophfit.fitting.error_models module clophfit.fitting.errors module clophfit.fitting.models module clophfit.fitting.odr module clophfit.fitting.pipeline module clophfit.fitting.plotting module clophfit.fitting.residuals module clophfit.fitting.utils module clophfit.prenspire module clophfit.prenspire.prenspire module clophfit.prtecan module clophfit.prtecan.export module clophfit.prtecan.models module clophfit.prtecan.parsers module clophfit.prtecan.titration module clophfit.testing module clophfit.testing.evaluation module clophfit.testing.fitter_test_utils module clophfit.testing.synthetic module clophfit.utils module ClopHfitError collect_multi_residuals() (in module clophfit.fitting.residuals) compare_methods_statistical() (in module clophfit.testing.evaluation) ComprehensiveErrorModel (class in clophfit.fitting.error_models) compute_all() (clophfit.prtecan.titration.TitrationResults method) compute_correlation_matrices() (in module clophfit.fitting.residuals) compute_residual_covariance() (in module clophfit.fitting.residuals) compute_variance() (clophfit.fitting.error_models.ComprehensiveErrorModel method) (clophfit.fitting.error_models.ConstantErrorModel method) (clophfit.fitting.error_models.ErrorModel method) (clophfit.fitting.error_models.ProportionalErrorModel method) concatenate_data() (clophfit.fitting.data_structures.Dataset method) ConstantErrorModel (class in clophfit.fitting.error_models) ConvergenceError copy() (clophfit.fitting.data_structures.Dataset method) create_dataset_dict() (clophfit.prtecan.titration.Titration method) create_ds() (clophfit.prtecan.titration.Titration method) create_global_ds() (clophfit.prtecan.titration.Titration method) CSV_F fit-titration-spec command line option ppr-enspire command line option CsvLineError ctrl (clophfit.prtecan.models.PlateScheme property) D data (clophfit.prtecan.models.Labelblock attribute) (clophfit.prtecan.models.LabelblocksGroup property) (clophfit.prtecan.titration.Titration property) DATA_DIR ppr-detect-bad-wells command line option data_nrm (clophfit.prtecan.models.Labelblock attribute) (clophfit.prtecan.models.LabelblocksGroup property) DataArray (class in clophfit.fitting.data_structures) dataframe (clophfit.prtecan.titration.TitrationResults property) dataframes (clophfit.prtecan.titration.Buffer property) dataframes_nrm (clophfit.prtecan.titration.Buffer property) Dataset (class in clophfit.fitting.data_structures) dataset (clophfit.fitting.data_structures.FitResult attribute) DataValidationError detect_adjacent_correlation() (in module clophfit.fitting.residuals) detect_and_discard_bad_wells() (clophfit.prtecan.titration.Titration method) detect_bad (clophfit.prtecan.titration.TecanConfig attribute) detect_bad_wells() (in module clophfit.fitting.diagnostics) detect_bad_wells_from_dat() (in module clophfit.fitting.diagnostics) dilution_correction() (in module clophfit.prtecan.parsers) discard (clophfit.prtecan.models.PlateScheme property) discard_bad_wells (clophfit.prtecan.titration.TitrationConfig attribute) distribute_axes() (in module clophfit.fitting.plotting) E empty (clophfit.prtecan.titration.BufferFit property) EnspireFile (class in clophfit.prenspire.prenspire) ErrorModel (class in clophfit.fitting.error_models) estimate_x_shift_statistics() (in module clophfit.fitting.residuals) evaluate_residuals() (in module clophfit.testing.evaluation) export() (clophfit.fitting.data_structures.Dataset method) export_bad_wells() (in module clophfit.prtecan.export) export_data() (clophfit.prtecan.titration.TitrationResults method) export_data_fit() (in module clophfit.prtecan.export) export_fit() (in module clophfit.prtecan.export) export_measurements() (clophfit.prenspire.prenspire.EnspireFile method) export_pngs() (clophfit.prtecan.titration.TitrationResults method) export_residuals() (in module clophfit.prtecan.export) extract_metadata() (in module clophfit.prtecan.parsers) extract_params() (in module clophfit.testing.evaluation) extract_residual_points() (in module clophfit.fitting.residuals) extract_sigma_df() (in module clophfit.fitting.plotting) F fgls_plate_fit() (in module clophfit.fitting.pipeline) figure (clophfit.fitting.data_structures.FitResult attribute) FILE fit-titration-glob command line option FileFormatError filename (clophfit.prtecan.models.Labelblock attribute) fit-titration command line option --is-ph --no-is-ph --out --verbose --version -o -v fit-titration-glob command line option --boot --no-weight --weight -b FILE fit-titration-spec command line option --band -b CSV_F NOTE_F fit_binding_glob() (in module clophfit.fitting.core) fit_binding_odr() (in module clophfit.fitting.odr) fit_binding_pymc() (in module clophfit.fitting.bayes) fit_binding_pymc_multi() (in module clophfit.fitting.bayes) fit_gain_and_rel_error_from_residuals() (in module clophfit.fitting.utils) fit_keys (clophfit.prtecan.titration.Titration property) fit_noise_model_from_residuals() (in module clophfit.fitting.utils) fit_plate() (in module clophfit.fitting.pipeline) fit_rel_error_from_residuals() (in module clophfit.fitting.utils) fit_trendline() (in module clophfit.fitting.utils) FitError FitResult (class in clophfit.fitting.data_structures) flag_trend_outliers() (in module clophfit.fitting.utils) format_estimate() (in module clophfit.fitting.odr) from_da() (clophfit.fitting.data_structures.Dataset class method) fromlistfile() (clophfit.prtecan.titration.Titration class method) G generalized_combined_model() (in module clophfit.fitting.odr) generate_combinations() (in module clophfit.prtecan.export) gsvd (clophfit.fitting.data_structures.SpectraGlobResults attribute) I identify_outliers_zscore() (in module clophfit.fitting.utils) InsufficientDataError InvalidDataError is_ph (clophfit.fitting.data_structures.Dataset attribute) (clophfit.prtecan.titration.Titration attribute) is_valid() (clophfit.fitting.data_structures.FitResult method) K k_from_result() (in module clophfit.testing.fitter_test_utils) kd() (in module clophfit.fitting.models) KD1 clop-eq1 command line option L label (clophfit.fitting.residuals.ResidualPoint attribute) Labelblock (class in clophfit.prtecan.models) labelblocks (clophfit.prtecan.models.Tecanfile attribute) LabelblocksGroup (class in clophfit.prtecan.models) labelblocksgroups (clophfit.prtecan.models.TecanfilesGroup attribute) lines (clophfit.prtecan.models.Labelblock attribute) LIST_FILE ppr-tecan command line option load_additions() (clophfit.prtecan.titration.Titration method) load_real_data_paths() (in module clophfit.testing.evaluation) load_scheme() (clophfit.prtecan.titration.Titration method) lookup_listoflines() (in module clophfit.utils) M make_benchmark_dataset() (in module clophfit.testing.synthetic) make_dataset() (in module clophfit.testing.synthetic) make_simple_dataset() (in module clophfit.testing.synthetic) ManyLinesFoundError mask (clophfit.fitting.data_structures.DataArray property) mask_outliers (clophfit.prtecan.titration.TitrationConfig attribute) measurements (clophfit.prenspire.prenspire.EnspireFile attribute) merge_md() (in module clophfit.prtecan.parsers) Metadata (class in clophfit.prtecan.parsers) metadata (clophfit.prenspire.prenspire.EnspireFile attribute) (clophfit.prtecan.models.Labelblock attribute) (clophfit.prtecan.models.LabelblocksGroup attribute) (clophfit.prtecan.models.Tecanfile attribute) (clophfit.prtecan.models.TecanfilesGroup attribute) mini (clophfit.fitting.data_structures.FitResult attribute) MiniProtocol (class in clophfit.fitting.data_structures) MissingDependencyError module clophfit clophfit.clophfit_types clophfit.fitting clophfit.fitting.bayes clophfit.fitting.core clophfit.fitting.data_structures clophfit.fitting.diagnostics clophfit.fitting.error_models clophfit.fitting.errors clophfit.fitting.models clophfit.fitting.odr clophfit.fitting.pipeline clophfit.fitting.plotting clophfit.fitting.residuals clophfit.fitting.utils clophfit.prenspire clophfit.prenspire.prenspire clophfit.prtecan clophfit.prtecan.export clophfit.prtecan.models clophfit.prtecan.parsers clophfit.prtecan.titration clophfit.testing clophfit.testing.evaluation clophfit.testing.fitter_test_utils clophfit.testing.synthetic clophfit.utils N n_sd() (clophfit.prtecan.titration.TitrationResults method) names (clophfit.prtecan.models.PlateScheme property) nofit_keys (clophfit.prtecan.models.PlateScheme property) noise_alpha (clophfit.prtecan.titration.TitrationConfig attribute) noise_gain (clophfit.prtecan.titration.TitrationConfig attribute) NOTE note_to_csv command line option Note (class in clophfit.prenspire.prenspire) NOTE_F fit-titration-spec command line option ppr-enspire command line option note_to_csv command line option --labels --output --temp -l -o -t NOTE O outlier() (in module clophfit.fitting.odr) outlier_scores_extended() (in module clophfit.fitting.utils) outlier_threshold (clophfit.prtecan.titration.TitrationConfig attribute) P params (clophfit.prtecan.titration.Titration property) parse_remove_outliers() (in module clophfit.fitting.utils) PH clop-eq1 command line option PKA clop-eq1 command line option PlateScheme (class in clophfit.prtecan.models) plot() (clophfit.fitting.data_structures.Dataset method) (clophfit.prtecan.titration.Buffer method) plot_autovalues() (in module clophfit.fitting.plotting) plot_autovectors() (in module clophfit.fitting.plotting) plot_emcee() (in module clophfit.fitting.plotting) plot_emcee_k_on_ax() (in module clophfit.fitting.plotting) plot_fit() (in module clophfit.fitting.plotting) plot_fit_gemini() (in module clophfit.fitting.plotting) plot_k() (clophfit.prtecan.titration.TitrationResults method) plot_pca() (in module clophfit.fitting.plotting) plot_qc_mean_vs_std() (in module clophfit.fitting.plotting) plot_qc_span_vs_center() (in module clophfit.fitting.plotting) plot_qc_span_vs_center_titration() (in module clophfit.fitting.plotting) plot_residual_vs_predicted() (in module clophfit.fitting.residuals) plot_residual_vs_yerr() (in module clophfit.fitting.residuals) plot_spectra() (in module clophfit.fitting.plotting) plot_spectra_distributed() (in module clophfit.fitting.plotting) plot_temperature() (clophfit.prtecan.titration.Titration method) PlotParameters (class in clophfit.fitting.plotting) ppr command line option --out --quiet --verbose --version -o -q -v ppr-detect-bad-wells command line option --ctr-cols --z-threshold DATA_DIR ppr-enspire command line option -b CSV_F NOTE_F ppr-tecan command line option --add --all --bg --bg-adj --bg-mth --cl --ctr-free-k --detect-bad --discard-bad-wells --dry-run --fit --fit-method --lim --mask-outliers --mcmc --mcmc-samples --no-detect-bad --no-discard-bad-wells --no-fit --no-mask-outliers --no-png --noise-alpha --noise-gain --nrm --nuts-sampler --outlier --outlier-threshold --png --sch --title -t LIST_FILE pprint() (clophfit.fitting.data_structures.FitResult method) predicted (clophfit.fitting.residuals.ResidualPoint attribute) prepare_output_folder() (in module clophfit.prtecan.export) print_emcee() (in module clophfit.fitting.plotting) process_trace() (in module clophfit.fitting.bayes) ProportionalErrorModel (class in clophfit.fitting.error_models) R raw_i (clophfit.fitting.residuals.ResidualPoint attribute) read_xls() (in module clophfit.utils) resid_raw (clophfit.fitting.residuals.ResidualPoint attribute) resid_weighted (clophfit.fitting.residuals.ResidualPoint attribute) residual_dataframe() (in module clophfit.fitting.residuals) residual_statistics() (in module clophfit.fitting.residuals) ResidualPoint (class in clophfit.fitting.residuals) result (clophfit.fitting.data_structures.FitResult attribute) reweight_from_residuals() (in module clophfit.fitting.utils) roughness() (in module clophfit.fitting.utils) run_pre_fit_detection() (in module clophfit.prtecan.export) S s_from_result() (in module clophfit.testing.fitter_test_utils) scheme (clophfit.prtecan.titration.Titration property) set_callback() (clophfit.prtecan.titration.TitrationConfig method) smoothness() (in module clophfit.fitting.utils) SpectraGlobResults (class in clophfit.fitting.data_structures) strip_lines() (in module clophfit.utils) svd (clophfit.fitting.data_structures.SpectraGlobResults attribute) T TecanConfig (class in clophfit.prtecan.titration) Tecanfile (class in clophfit.prtecan.models) TecanfilesGroup (class in clophfit.prtecan.models) TecanFitCombination (class in clophfit.testing.fitter_test_utils) Titration (class in clophfit.prtecan.titration) TitrationConfig (class in clophfit.prtecan.titration) TitrationResults (class in clophfit.prtecan.titration) titrations (clophfit.prenspire.prenspire.Note attribute) TruthParams (class in clophfit.testing.synthetic) U unit (clophfit.prtecan.parsers.Metadata attribute) V validate_residuals() (in module clophfit.fitting.residuals) verbose (clophfit.prenspire.prenspire.EnspireFile attribute) (clophfit.prenspire.prenspire.Note attribute) verbose_print() (in module clophfit.prenspire.prenspire) W weight_da() (in module clophfit.fitting.core) weight_multi_ds_titration() (in module clophfit.fitting.core) weights_from_sigma() (in module clophfit.utils) wells (clophfit.prenspire.prenspire.EnspireFile attribute) (clophfit.prenspire.prenspire.Note attribute) (clophfit.prtecan.titration.Buffer property) X x (clophfit.fitting.data_structures.DataArray property) (clophfit.fitting.residuals.ResidualPoint attribute) x_err (clophfit.fitting.data_structures.DataArray property) (clophfit.prtecan.titration.Titration attribute) Y y (clophfit.fitting.data_structures.DataArray property) y_err (clophfit.fitting.data_structures.DataArray property) (clophfit.fitting.residuals.ResidualPoint attribute)