Index A | B | C | D | F | G | I | K | M | P | R | S | T | U | V | X A additional_information (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) aggregate() (in module pyXLMS.transform) alpha_decoy (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) alpha_modifications (pyXLMS.data.CrosslinkSpectrumMatch attribute) alpha_peptide (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) alpha_peptide_crosslink_position (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) alpha_proteins (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) alpha_proteins_crosslink_positions (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) alpha_proteins_peptide_positions (pyXLMS.data.CrosslinkSpectrumMatch attribute) alpha_score (pyXLMS.data.CrosslinkSpectrumMatch attribute) AMINO_ACIDS (in module pyXLMS.constants) AMINO_ACIDS_1TO3 (in module pyXLMS.constants) AMINO_ACIDS_3TO1 (in module pyXLMS.constants) AMINO_ACIDS_REPLACEMENTS (in module pyXLMS.constants) annotate_fdr() (in module pyXLMS.transform) annotate_string_scores() (in module pyXLMS.transform) assert_csms() (in module pyXLMS.transform) assert_csms_or_xls() (in module pyXLMS.transform) assert_data_type_same() (in module pyXLMS.transform) assert_xls() (in module pyXLMS.transform) B beta_decoy (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) beta_modifications (pyXLMS.data.CrosslinkSpectrumMatch attribute) beta_peptide (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) beta_peptide_crosslink_position (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) beta_proteins (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) beta_proteins_crosslink_positions (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) beta_proteins_peptide_positions (pyXLMS.data.CrosslinkSpectrumMatch attribute) beta_score (pyXLMS.data.CrosslinkSpectrumMatch attribute) C charge (pyXLMS.data.CrosslinkSpectrumMatch attribute) check_available_keys() (in module pyXLMS.transform) check_indexing() (in module pyXLMS.data) check_input() (in module pyXLMS.data) check_input_multi() (in module pyXLMS.data) completeness (pyXLMS.data.Crosslink property) (pyXLMS.data.CrosslinkSpectrumMatch property) (pyXLMS.data.ParserResult property) copy_with_update() (pyXLMS.data.Crosslink method) (pyXLMS.data.CrosslinkSpectrumMatch method) (pyXLMS.data.ParserResult method) create_crosslink() (in module pyXLMS.data) create_crosslink_from_csm() (in module pyXLMS.data) create_crosslink_min() (in module pyXLMS.data) create_csm() (in module pyXLMS.data) create_csm_min() (in module pyXLMS.data) create_parser_result() (in module pyXLMS.data) Crosslink (class in pyXLMS.data) crosslink_spectrum_matches (pyXLMS.data.ParserResult attribute) crosslink_type (pyXLMS.data.Crosslink property) (pyXLMS.data.CrosslinkSpectrumMatch property) CROSSLINKERS (in module pyXLMS.constants) crosslinks (pyXLMS.data.ParserResult attribute) CrosslinkSpectrumMatch (class in pyXLMS.data) csms() (pyXLMS.data.ParserResult method) D data_type (pyXLMS.data.Crosslink property) (pyXLMS.data.CrosslinkSpectrumMatch property) (pyXLMS.data.ParserResult property) detect_plink_filetype() (in module pyXLMS.parser) detect_scout_filetype() (in module pyXLMS.parser) detect_xi_filetype() (in module pyXLMS.parser) display() (in module pyXLMS.transform) (pyXLMS.data.Crosslink method) (pyXLMS.data.CrosslinkSpectrumMatch method) (pyXLMS.data.ParserResult method) F fasta_title_to_accession() (in module pyXLMS.transform) filter_crosslink_type() (in module pyXLMS.transform) filter_peptide_pair_distribution() (in module pyXLMS.transform) filter_protein_distribution() (in module pyXLMS.transform) filter_proteins() (in module pyXLMS.transform) filter_residue_pair_distribution() (in module pyXLMS.transform) filter_target_decoy() (in module pyXLMS.transform) format_sequence() (in module pyXLMS.parser) from_dataframe() (in module pyXLMS.transform) from_json() (in module pyXLMS.transform) G get_available_keys() (in module pyXLMS.transform) get_bool_from_value() (in module pyXLMS.parser) get_msannika_crosslink_sequence() (in module pyXLMS.exporter) get_string_ids() (in module pyXLMS.transform) get_string_network() (in module pyXLMS.transform) I intersection() (in module pyXLMS.transform) ion_mobility (pyXLMS.data.CrosslinkSpectrumMatch attribute) items() (pyXLMS.data.Crosslink method) (pyXLMS.data.CrosslinkSpectrumMatch method) (pyXLMS.data.ParserResult method) K keys() (pyXLMS.data.Crosslink method) (pyXLMS.data.CrosslinkSpectrumMatch method) (pyXLMS.data.ParserResult method) M MEROX_MODIFICATION_MAPPING (in module pyXLMS.constants) model_config (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) (pyXLMS.data.ParserResult attribute) model_post_init() (pyXLMS.data.Crosslink method) (pyXLMS.data.CrosslinkSpectrumMatch method) MODIFICATIONS (in module pyXLMS.constants) modifications_to_str() (in module pyXLMS.transform) module pyXLMS pyXLMS.constants pyXLMS.data pyXLMS.exporter pyXLMS.parser pyXLMS.pipelines pyXLMS.plotting pyXLMS.transform P parse_modifications_from_maxquant_sequence() (in module pyXLMS.parser) parse_modifications_from_scout_sequence() (in module pyXLMS.parser) parse_modifications_from_xi_sequence() (in module pyXLMS.parser) parse_peptide() (in module pyXLMS.parser) parse_scan_nr_from_mzid() (in module pyXLMS.parser) parse_scan_nr_from_plink() (in module pyXLMS.parser) parse_spectrum_file_from_plink() (in module pyXLMS.parser) ParserResult (class in pyXLMS.data) pipeline() (in module pyXLMS.pipelines) plot_crosslink_type_distribution() (in module pyXLMS.plotting) plot_peptide_pair_distribution() (in module pyXLMS.plotting) plot_protein_distribution() (in module pyXLMS.plotting) plot_residue_pair_distribution() (in module pyXLMS.plotting) plot_score_distribution() (in module pyXLMS.plotting) plot_string_score_distribution() (in module pyXLMS.plotting) plot_target_decoy_distribution() (in module pyXLMS.plotting) plot_venn_diagram() (in module pyXLMS.plotting) pyXLMS module pyXLMS.constants module pyXLMS.data module pyXLMS.exporter module pyXLMS.parser module pyXLMS.pipelines module pyXLMS.plotting module pyXLMS.transform module pyxlms_modification_str_parser() (in module pyXLMS.parser) R read() (in module pyXLMS.parser) read_custom() (in module pyXLMS.parser) read_maxlynx() (in module pyXLMS.parser) read_maxquant() (in module pyXLMS.parser) read_merox() (in module pyXLMS.parser) read_msannika() (in module pyXLMS.parser) read_mzid() (in module pyXLMS.parser) read_plink() (in module pyXLMS.parser) read_scout() (in module pyXLMS.parser) read_xi() (in module pyXLMS.parser) read_xinet() (in module pyXLMS.parser) read_xiview() (in module pyXLMS.parser) read_xlinkx() (in module pyXLMS.parser) reannotate_decoy_labels() (in module pyXLMS.transform) reannotate_positions() (in module pyXLMS.transform) retention_time (pyXLMS.data.CrosslinkSpectrumMatch attribute) S scan_nr (pyXLMS.data.CrosslinkSpectrumMatch attribute) score (pyXLMS.data.Crosslink attribute) (pyXLMS.data.CrosslinkSpectrumMatch attribute) SCOUT_MODIFICATION_MAPPING (in module pyXLMS.constants) search_engine (pyXLMS.data.ParserResult attribute) spectrum_file (pyXLMS.data.CrosslinkSpectrumMatch attribute) summary() (in module pyXLMS.transform) T targets_only() (in module pyXLMS.transform) to_alphalink2() (in module pyXLMS.exporter) to_crosslink() (pyXLMS.data.CrosslinkSpectrumMatch method) to_dataframe() (in module pyXLMS.transform) to_impxfdr() (in module pyXLMS.exporter) to_json() (in module pyXLMS.transform) to_msannika() (in module pyXLMS.exporter) to_proforma() (in module pyXLMS.transform) (pyXLMS.data.Crosslink method) (pyXLMS.data.CrosslinkSpectrumMatch method) to_proxl() (in module pyXLMS.exporter) to_pyxlinkviewer() (in module pyXLMS.exporter) to_xifdr() (in module pyXLMS.exporter) to_xinet() (in module pyXLMS.exporter) to_xiview() (in module pyXLMS.exporter) to_xlinkdb() (in module pyXLMS.exporter) to_xlmstools() (in module pyXLMS.exporter) to_xmas() (in module pyXLMS.exporter) U unique() (in module pyXLMS.transform) V validate() (in module pyXLMS.transform) values() (pyXLMS.data.Crosslink method) (pyXLMS.data.CrosslinkSpectrumMatch method) (pyXLMS.data.ParserResult method) venn() (in module pyXLMS.plotting) X XI_MODIFICATION_MAPPING (in module pyXLMS.constants) xls() (pyXLMS.data.ParserResult method)
