pyXLMS package

Subpackages

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

Module contents

A python package to process protein cross-linking data.