Index A | B | C | D | E | F | G | I | L | M | P | S A add_current_data_point() (proteobench.modules.template.module.Module method) B benchmarking() (proteobench.modules.template.module.Module method) C calculate_benchmarking_metric_1() (proteobench.modules.template.datapoint.Datapoint method) calculate_benchmarking_metric_2() (proteobench.modules.template.datapoint.Datapoint method) convert_to_standard_format() (proteobench.modules.template.parse.ParseInputs method) D Datapoint (class in proteobench.modules.template.datapoint) dump_json_object() (proteobench.modules.template.datapoint.Datapoint method) E enzyme_name (proteobench.modules.template.datapoint.Datapoint attribute) F fdr_peptide (proteobench.modules.template.datapoint.Datapoint attribute) fdr_protein (proteobench.modules.template.datapoint.Datapoint attribute) fdr_psm (proteobench.modules.template.datapoint.Datapoint attribute) fragment_tol (proteobench.modules.template.datapoint.Datapoint attribute) fragment_tol_unit (proteobench.modules.template.datapoint.Datapoint attribute) G generate_datapoint() (proteobench.modules.template.module.Module method) generate_id() (proteobench.modules.template.datapoint.Datapoint method) generate_intermediate() (proteobench.modules.template.module.Module method) I id (proteobench.modules.template.datapoint.Datapoint attribute) is_implemented() (proteobench.modules.template.module.Module method) is_temporary (proteobench.modules.template.datapoint.Datapoint attribute) L load_input_file() (proteobench.modules.template.module.Module method) M max_pep_length (proteobench.modules.template.datapoint.Datapoint attribute) MBR (proteobench.modules.template.datapoint.Datapoint attribute) min_pep_length (proteobench.modules.template.datapoint.Datapoint attribute) missed_cleavages (proteobench.modules.template.datapoint.Datapoint attribute) module proteobench.modules.template.datapoint proteobench.modules.template.module proteobench.modules.template.parse proteobench.modules.template.parse_settings proteobench.modules.template.plot Module (class in proteobench.modules.template.module) P ParseInputs (class in proteobench.modules.template.parse) ParseSettings (class in proteobench.modules.template.parse_settings) plot_bench1() (in module proteobench.modules.template.plot) plot_bench2() (in module proteobench.modules.template.plot) precursor_tol (proteobench.modules.template.datapoint.Datapoint attribute) precursor_tol_unit (proteobench.modules.template.datapoint.Datapoint attribute) proteobench.modules.template.datapoint module proteobench.modules.template.module module proteobench.modules.template.parse module proteobench.modules.template.parse_settings module proteobench.modules.template.plot module S search_engine (proteobench.modules.template.datapoint.Datapoint attribute) software_version (proteobench.modules.template.datapoint.Datapoint attribute)